You are forgetting that you also lose whatever the very last ability you would have gotten to use on the boss is. Supposing in the last 1.5 seconds of the boss fight you were going to be using a SS. Now, because you waited an extra 1.5 seconds to reapply PS earlier on in that fight you no longer get to use that extra final SS. So the cost to gain an extra disease tick is 10% of a PS + 100% of a SS.

So in a fight that lasts 280 seconds (14 full rotations) you end up waiting an extra 14 * 1.5 = 21 seconds overall to reapply PS. That costs you one full rotation in lost time or 1/14th of your overall special ability usage. Now it doesn't sound so good. The reality however is twice as bad as that and you will, end up losing twice as much time.

This is due to the seldom considered two-second rule. You see if you use your runes within 2 seconds of them coming off cooldown they go back on cooldown as if you had used them the moment they came off cooldown. If it goes beyond that then they go back on cooldown as you would expect. So in a normal rotation your runes come off cooldown like (assume this shows runes coming off cooldown after your first rotation, so this starts 20 seconds into the fight).

Where every row is 1 gcd (generalising to 7 gcds per 10 seconds which is near enough to accurate). What you see is that in the second rotation, even though you used the first two runes for a SS after the U rune came off CD the F rune went back onto cooldown as if you had used it immediately. This is due to the two second rule. The same happens to the two blood runes. Even though you use them at the same instant for a SS when they come back as D runes, the first one goes back on CD with 1 GCD less time to go because you managed to use it within 2 seconds of coming off cooldown. So you get through the entire rotation in 14 GCDs and are ready to start over.

Now, lets add in the extra GCD you are waiting to renew that blood plague.
The first * indicates the GCD you waste waiting before using your U rune to reapply blood plague. The second * indicates the extra GCD you lose because you didn't use your F rune within 2 seconds of it coming off of GCD. So the overall cost to you is that each rotation takes an extra 2 global cooldowns, you are going from 14 to 16 GDCs, the total cost over time will be 1/7th of your total ability usage. In short, waiting an extra 1.5 seconds for that last tick of EP is a very bad thing to do and will cost you a lot of DPS.

Since disease re-apping is coming up I thought I would contribute, this isn't something that can be simmed its just using basic knowledge in reapplying them.

I like to call it Disease Juggling

When your disease just ticked for the 18s mark, refreshing the disease that just ticked will allow your other disease to tick before you refresh it, due to it being a gcd away, and diseases being 1.5s apart. Note that this can't be applied to every 20s segment, but rather close to it.

Below is some data from our logs displaying the situation, read it carefully and see if you understand

And another example

As you can see in the data from the logs, for instance the second one since only 4 parts are bolded, it started with a PS / IT combo, but ended with a IT / PS combo, allowing for the extra disease tick in between the refresh at [19:37:16.093]

Over a fight this can contribute to quite a few extra disease ticks, and how I go about refreshing mine, I made this image a while ago to try and demonstrate it, but I think I explained it quite well with the logs, just for reference.

I see alot of people just solely sticking to a rotation and refreshing diseases in that order, losing potential ticks.

One thing you need to consider when thinking about not clipping diseases, is whether or not your raid has another source of a magic debuff. If not, clipping your diseases is almost 100% necessary, as the minimal DPS gained by not clipping will be greatly overshadowed by the raid DPS lost by not having ebon plague up.

That looks roughly right, it'll depend on your latency extra rp etc. While it's a nominal DPS improvement. You'd probably get more out of disease twisting even if you screw up a bit.

For the sim of twisting diseases I just used an initial sequence of IT PS SS BS BS (dump)
Then a repeating sequence of (2x) SS SS (PS IT) (dump) // SS SS BS BS (more dump)
Where the diseases are swapped for the second cycle.
In practice for many fights you can't run a perfect rotation but it's pretty easy to line up your disease refreshes to maximise the number of ticks you get.

Eventually's pic sums it up. The only thing you have to be a bit careful of is the timing, but if you're using death runes to apply the diseases it's actually quite forgiving on that (so you can sneak in extra dumps).

That's true only if you drop a point from epidemic and naively apply the diseases.
You can however setup a rotation (especially in a reaping build), so your diseases are offset by more than 3 seconds so you never lose EP. Under some circumstances there are certain advantages to doing so. (You can get better uptime on your 2T9 bonus if you spread out your BS more).

ETA:
As an aside I wonder how much damage you have to in general to make it worth delaying your rotation by 1 gcd permanently. A rough calculation using data from my most recent sims tends to suggest that in BiS gear our strikes plus DC dumps do about 5K dps. So using a GCD do to an extra DC would have to do about 7.5K damage to even be considered as worth it. (given your average damage cycle is top heavy). The DC + UB hits for about 7.15K damage. So it's a small loss (but that was without morbidity). (With full morbidity it comes out at a win). Of course that assumes the RP would be wasted otherwise.

If you disease juggle, ebon plague has 100% uptime.

Delaying runes is generally bad, but there are beneficial occasions. You can delay them for a DC, when you're a maximum rp. Saving your D rune pair exclusively for a SS is also worth it. I just tested that with a modified sim.

I don't see how it could be worth it. If you wait 1 extra GCD to use your two D runes then you are bring the first D rune out of the two second rule. This means you have to wait 3 seconds more to use your blood strike on the next rotation. If the runic power was going to be lost due to going overcap if you didn't use them then maybe it would be a DPS gain, but if not then I don't see it being a DPS gain. Maybe theres something I am missing.

We have a frost and another unholy dk in the raid, there should always be blood plague on the target.

You never reapply diseases at the 15s mark, you juggle them in the 18s - 21s window, depending on the previous disease used you will get the 18s tick from one, refresh the one that did the 18s tick, then automatically the 21s will tick from the other due to it being 1.5s apart, this method also allows quick refresh times on diseases.

Its just something you get the hang of, try it out on a dummy for a bit and see if it makes sense. You never waste any rune delay.

I think the question is more, where do you get the unholy rune from ?

I haven't checked it yet, so maybe the rune is back up in 18 seconds, but i generally find that when my frost rune comes back up, FF is on 1 sec and my unholy rune i still on cooldown.

Let me show you what i mean:

t=	Rune type	Ability	Back up at t=
0	F	IT	10
1.5	U	PS	11.5
3-10	-	Other strikes	-
10	F	Hold for U rune	-
11.5	U	Scourge strike	F at 20; U at 21.5

And this is the problem i see.
I do the normal SS>SS>SS rotation between the 10 to 20 second mark.

After that the frost rune comes back up at 20 seconds, but there is no unholy rune available until 21.5.

That means that either:
1) You are skipping the last scourge strike and use that blood rune
2) You refresh PS at t=21.5 second, since it started at t=1.5, its on the 20 second mark and 1 second from the last tick and 2 seconds after the previous tick. Which also means you lose out a few seconds on frost fever
3) Your general rotation is delayed. Because that's the only way i can see i can see that SS at t=11.5 have the 2 second leeway. It SHOULDN'T if your rotation is on the ball since the unholy rune hasn't been "waiting".
4) I'm missing something very obvious.

Please enlighten me though how you can use unholy rune before a frost rune when they come up in a different order.

I use empower rune weapon at the start on my first gargoyle to make up for the rp loss from summon to dc, this causes the unholy / frost runes that you would normally use to redisease to always refresh at the same time for the rest of the fight, allowing you to juggle.

I didn't actually notice that till I just tested it on a dummy, since I always empower the same way on every fight.

edit: Or like the poster below me posted, using a 2nd set set of runes to refresh that come up at the same time, I prefer creating my own ones with ERW, but that technique also gets the job done!

I also found the easiest way to do it by using ERW at the start, which I always do for the same reason as Potlol; there's no RP to dump after summoning Gargoyle. Using ERW makes the juggling possible without using your death runes for it, as the UF runes will come off CD at the same time.
What can mess this up is a missed IT or a dodged PS, which make your U and F runes go out of sync. If that happens you need to switch the runes you use for reapplying diseases, or start clipping normally for the rest of the fight.
Juggling gives your EP 100% uptime, but your BP drops off every second rotation, which is why you should clip normally when there's no other DK's present to gain the benefit from RoR.

Starter:
PS-IT-BS-BS-SS Gargoyle+ERW
SS-SS-SS Dump

Rotation:
(IT<->PS)-SS-BS-BS Dump
SS-SS-SS Dump

I'd like to see math on 1/2 Epidemic vs. disease juggling, but I'm guessing the latter is superior.
Atleast with another Unholy DK present to keep EP and BP up, 1/2 Epidemic seems to win against the normal disease clipping rotation by ~40 DPS on the sim for me, but I don't know if it's possible to sim disease juggling, which is why I'd like to see some math on it.

As we are able to soak RP on most of the fights, doesn't that make 12/0/59 with 2 points in Morbidity a better choice than 14/0/57? As the difference with no extra RP is only a few DPS on 14/0/57's favor.
If your Druids are speccing into Revitalize, that would favor 12/0/59 even more. There's also the reduced CD on DnD, which doesn't really matter on ICC bosses, but is great for trash/adds and Anub. What are your thoughts and opinions on this and what is still keeping people using 14/0/57?