I can confirm your fury spec but need to look at the other 2 more closely as to why it was reported as a loss of dps. I added your fury changes to release.
I can verify that using the annihilation and carnage spec as posted is a dps loss in pve; they gave me a high number in pvp which is what I tweaked them for. I'll throw my thought process down on how I put the rotation in there in hopes I can learn more to make them better.
Annihilation:
In it's current form (as I posted) I placed "smash" into the normal rotation because with buddywing, the AoE flag is not recognized in pvp. I assume the targetting system does not understand other players as groups of NPC's. With Annihilation spec, smash is one of the top priorities in pvp after bleeds due to the fact that you're almost always in heavy groups of players if playing the spec properly IMO. Just an FYI, this routine with my changes has netted me 6-7k dps games with this spec; I hold the current unofficial server record in dps using this. It's insane how much more than other people I do with it in PvP. Where the second best guy is sitting at 2 mil total dmg (merc) i'll be top with like 5 mil. My focus was to ensure annihilation and Force Rend are used whenever avail and that NO filler is used with the target does not have rupture bleed. Then Smash is always used off CD when a target had a bleed effect. This basically keeps bleeds on the target, uses annihilate and spreads dots with smash constantly. Works amazing for me!
In PvE it's a different story, smash is not used and the AoE flag works so smash can be accounted for with the AoE rules (3 or more targets). I included my PvE version of annihilation.cs and you will definitely have better PvE dps with it. I am currently ranked top 5 overall on parsley with this routine as annihilation on the operations target dummy.
My changes look messy and there are alot of repeating, in my experience if I don't keep placing annihilate and force rend after every ability the routine with get stuck using vicious slash or assault way too often. In order for annihilation to shine, dots need to always be applied and annihilate needs to be uses off CD.
Carnage:
For some reason, buddywing has issues on my PC when using a high alac build. Sometimes I notice the animation getting stuck; I am having much better luck with these changes for PvP and PvE. My original carnage.cs posted earlier was a PvE DPS loss because I had several abilities like Gore and Viscous Throw outside of the Ferocity window. I feel that in PvP having a gore debuff always on the target is more important than ensuring it's available in the ferocity window. These new changes posted below are giving me 8.8k pve dps currently with this spec. The changes are for PvE and force Gore, Viscous Throw, Ravage, and Devastating Blast into the ferocity window and using Massacre as filler and then Bat Assault/Assault to build rage when needed. I still struggle with this though, sometimes my character gets stuck in an animation loop and I don't know if it's lag on my end or buddywing causing it.
Enough of my rambling...let me know if these changes work better or worse for you in PvE! I can assure you though, my original scripts posted are amazing in PvP! I know that PvP is not really where the focus of Buddywing is but I just love it. Objective based combat is important so being able to take my eyes and attention away from my rotation and see what other players are doing or who's trying to cap/off-heal is a big deal and makes these routines shine. I am new to Buddywing myself but thus far I am so appreciative of it and really excited to use it. I remember how much the honorbuddy routines made me love WoW.
P.S. Posted them in a zip because it wouldn't let me upload a .cs file.