If you respec from BM to MM (or I believe to SV), you may end up with a pet talent tree like this:
The pet talents used with the BM spec remain in the tree, preventing the use of the new unspent talents on, say, Thunderstomp. The BM talents only exist in the talent tree and not in the pet’s Spellbook, though. Essentially, you are left with an animal friend that does not have and cannot obtain any of the pet talents you assigned to it when you were BM.
There is an easy fix: just go to a pet trainer and reset your pet’s talents. This is also the official fix.
-Eidotrope

I noticed this about 2-3 monthes back, I rerolled around that time for other reasons, but when I play my hunter now I feel like my pet is missing all the talent abilities and dps gains, maybe its just my lack of hunting as of late.
I also noticed this a few months ago. I hadn’t hit it in a while… I haven’t had to respec my pets in a while either. They retain their completely separate BM or SV allocations.
I noticed this some months back…and spent so much time talking with GM’s who had no clue how to fix it…I was ashamed when I figured out it was so easy.
Yep, had this happen to me as well. I put a ticket in and spoke with a GM about it.
That kind of bums me out cause I threw a ticket at the GMs about 4 monthes back now for this and 4days to a week later I got mail in my in game mailbox telling me to go read the forums, I was relatively upset cause I had never seen anything on the issue. I avoid the Blizz official forums though, /shrug.
Made a ticket about this issue yesterday morning, this morning I checked and Blizz sent me a standard message saying I should delete my WTF/Cache AND Interface folders because it probably had something to do with my custum UI .. I’m SO glad I surfed the web and found this solution, tried it and it worked, thanks a lot :D
Yes, if you report this bug, the first response you get will likely be one recommending that you clear your UI-related folders. Doing so will do nothing to solve the problem, though.