I can also confirm that this is happening in my build, however it's not only Hunter's pets that are not regenerating focus, but Warlock summons aren't regenerating as well.
From my observations the regeneration stops very frequently both in and out of battle. The hunter's pet focus gets used but does not regenerate back also the same for a Warlock's Imp summon, which doesn't regenerate it's mana. Sometimes it stops for only a few seconds, but often it stops for up to 5 minutes or longer from what I have seen.
Another thing I have noticed in my observations, though I'm not sure it's related to the same issue, is the Hunter pets will not do their normal attacks during this time as well. If I turn all of the pet's autocasts off except growl, then send it into a fight, the pet will just stand there doing nothing but autocast growl every time the cooldown time is over.
This has been happening since I first compiled and started up MaNGOS, and while it happens at random times, it happens very often leaving pet/summon regeneration disabled from seconds to minutes which really hinders pet/summon focused builds.
MaNGOS rev: 10995
UDB: 396
SD2: 1941
Custom Patches: AHBot