A few things that might explain the dip:

Your dps time (%) is lower.
Unleashed Rage has a lower uptime.
Expose Weakness has a lower uptime.
Retribution Aura has a lower uptime (8% vs 0%, but still)
1 fewer LnL proc.

It's probably not worth shifting through everything, but if you're really curious, take a look when your crits occur. Did more take place under UR and/or EW in the first attempt? I'd guess yes, since they were active for more of the fight. That might explain the difference in your damage ceiling.

EDIT: Wow, talk about not seeing the forest from the trees--I missed something fairly obvious at first glance. I'm going out on a limb (ha!) here and guessing you did, in fact, cast Steady Shot at least once during the second attempt. None are recorded and your other damage sources add up to 100%, so I'm betting there's a pretty significant error at work there.

Small world. SpartanUI is the brainchild of one of my guild's founders. Ansu doesn't really play that much anymore, but I think he still works on the UI project, which has its own team. If it turns out to be an issue, let me know. A lot of us (Spartans) use it.

Im going to vote on this one

In the last few weeks my dps wasnt as high as supposed ( 5500+ ) and i was always missing a few hundreds . I thought that its the lag, or maybe i dont have the best rotation, but then i found out and it was the range . When i stood at closer range to get a better uptime of some melee buffs, my dps increased nicely and i was getting the number that i was expected to get ( 5500 - 5700 dps )

Stay at closer range and ignore the sniper training, its not worth in comparison with the rest of the missing buffs and their uptime

PS : The thingy with staying at 30 yards and getting both sniper training/melee buffs doesnt really work as the melee players are mostly further than patchwerk itself

You sir are a genius. As part of changing my UI I messed up the steady shot macro. So Steady Shot was not firing even though I was pressing the button. Wow, I feel stupid.

However, it still doesn't account for the huge loss in explosive damage, that's a loss of 1.8k damage per explosive. I can't work out where that would come from.

I'm actually having a hard time understanding your question, but will try to answer it anyway.
First, it's hard to tell where things are happening without the actual WWS report. Also, what are these differences you are mentioning? Since they are in hundred thousand range, I'm assuming it's either from a boss kill or the collection of boss kills. Having a WWS report to look at would help.
From your explanation, it seems like you have better gear than the other two hunters, which would explain why your explosive shots hit harder. As for auto shot and steady shot number difference, I'm guessing that the other two hunters aren't using multi shot and/or have more haste than you. Since BiS gears don't really have much haste compared to others, it would change the number of auto shots made. Also, your rotation has you waiting only 1.5 sec, not 2sec, between the ES. This will clip last tick of explosive shot and may be one of the reasons why you have far less explosive shots recorded on WWS.
I'm confused about your question regarding armor pen. How can armor pen be valuable when you do better without them? It has been discussed in many threads that Armor Pen is a bad stat in terms of item budgeting and next patch only makes it just not as bad, but still not very good.

I will PM you a WWS since the guild doesn't want it to be tossed around.

waiting 1.5 Second to fire the ES should be fine because of travel time the shot should land in perfect syn and not clip the last tick. If it does I'll go back to using ES/Multi/ES/Steady

So I looked at your WWS. If you just look at all bosses, the numbers are pretty much the same for all shots. You also critted more than the other people on Explosive Shot, which explains why your damage from Explosive Shot is higher than the other two. Humera has the most haste, so that explains why he has more auto shot, but other shots occur in similar numbers. Also, your dps numbers are pretty close to each other.
If you look at say the whole WWS report, of course numbers will be off a lot since you cast volley, move around and do other stuff as well. Just looking at the boss kills, I really don't see anything wrong with it, considering how your gears are pretty close to each other.
As for waiting 1.5sec, if time between 2 explosive shot is 1.5 sec (i.e. spam ES), it'll definitely clip the last tick. Both shots have the same travel time, so if you fire them every 1.5 sec, they will land with 1.5sec difference. I didn't look at your combat log to see if clipping actually happens and it might not because of latency and such (.5 sec isn't all that long).

Regarding the Sniper Training/Melee buffs position, on fights like PW/loatheb at least it seems pretty moot, since trapdancing provides such a ridiculous damage boost, and requires you give up on ST. I usually get 8 procs per 2:50ish PW, compared to 2-3 when at Sniper Training range.

This week I got only 6 thanks to screwing up a bit, and lost a few hundred DPS, inspite of better gear than last week.

edit: ok, "a few hundred DPS" is exaggerating, mental math on the bus says each trapdanced LnL proc is a net gain of around 19k damage, while the two LnL procs I missed this week were worth about 30k damage total. So a net loss of 30000/170 = 176 DPS lost.

Still, if that napkin math is right (I couldn't remember the average auto and steady damage figures :S), going from 3 LnL procs per 2:50 fight with no trapdancing to 8 with trapdancing is equal to: 19000 x 5 / 170 = 558 dps lost?

You'd need to be doing 9300 dps from just steady, aimed and ES before the 6% damage from Sniper Training would gain you that much DPS. Of course you could get lucky and get an LnL proc every internal cooldown, that'd still be a total of only 5 LnL procs in 2:50.

At the risk of beating a dead horse here... I have searched this post and i remember seeing it somewhere but can not find it so here goes...

I have 407 haste and depending on some gear swaps of stuff in my bag I can get 470ish...

At 407 haste it shows 12.41% haste on the paperdoll.

With 15% from quiver and 12.41% haste from gear - at what point do you not need any points in IAotH ?

armory link -http://www.wowarmory.com/character-sheet.xml?r=Staghelm&n=Belbo

The haste softcap is 522.

Ummm, that cannot be correct. First off, the travel time it takes to land is the same as the shot prior (unless you moved a great distance) therefore if it took .5s for your first shot to land, it would be the same .5s for the 3nd shot to land.

Second of all, it is not waiting 1.5 Seconds to fire the subsequent ES's... ES ticks 2 additional times every second. Therefore it is 2 seconds that need to be accounted for. 1.5 seconds is handled by your GCD then another .5s "pause".

This is the 3rd time I've seen someone talk about "travel time" and I wonder where they got it from.