I seem to recall an issue with the exporter not being able to create more than one animation group in a nif, so if you wanted more than one, you'd export each animation separately and then combine them back into a single file with NifSkope. Is this a rough match to what you're trying to do?
At first I just modified a mesh I had made earlier and added the animations, when that did not work, I rebuild the mod from scratch, making sure to add the animations before I put it together.
--MNPred