No, the sim wait for the buff to fall to refresh it. For a 100hour fight, that 1200 segment of 5 min, so it's correct for the B case. I guess in rotation mode, the blood taped rune become desynchronized by a GCD and make a DPS loss as the sim wait a few second plus the fact that it don't have a 100% uptime. I will check the later.
Edit: New release
1.2.0.2 Release notes
* Correction on Priority editor.
* Weapon Dps scaling option added.
* Better Bone shield/UA usage when used after BloodStrike
* New buff: Frost Fever/Blood Plague from another deathknight.
* New Priority "FadeRime" to cast HB when Rime buff is about to fade.
* Haste EP Calculation: Calculation will take longer due to the the sim calculating at multiple value of haste to have more consistent value.
* Option Wait for FC modification: The flag will trigger when the AP of the character is greater than 80% of the maximum possible AP.
* Report DPS should contain back damaging proc.
Kahorie's DK Simulator 1.2.0.2