I'm not aware of any current bugs in reanimation manipulation (which isn't any proof there aren't any, of course). There was a bug a while back (fixed in version 0.33, according to my earlier post in this thread, while the current version being 0.36 [the version number is found on one of the help screens]).
The reanimation functionality works throughout the biome, i.e. it reanimates both the surface and the caverns below, both following the surface biome boundaries. Thralling works through evil clouds, which exist on the surface only. Note, however, that you have to make sure you embark in the modified biome, as world tiles often have parts of multiple biomes in them.
My main test is to embark, slaughter an animal, and see if its hide/hair reanimates, so I haven't taken much notice of wild animals.
I'm not aware of anything particular that can be done/is necessary to get reanimated animals, but there are unidentified fields all over the place in DF, so it wouldn't be impossible for this to be something that's not mapped (e.g. the nearby boolean fields unk_1e5 and unk_1e6, but they can be "true" when the region is neither evil nor reanimating, so they're probably not candidates. Other possibilities would be unidentified flags in the region map entries [where most of the world tile data resides]).
I haven't tried to correlate the Dead Percentage field to appearance of reanimated animals either, only to the amount of dead vegetation.
Short answer: The reanimating "weather" has been correlated with reanimation of slain creatures, with little to no notice taken to undead wildlife, although the assumption has been that both are controlled by the same field. If that's incorrect, further research is needed (or there's an unknown bug lurking in the script).