Could it be that you are not keying your node/animation/action // whatever by default?
If you change the properties of something to key them, you are changing the default properties without the animation node being able to know.
If you are going to use animation, the first thing I would do is key in frame 1 the 'thing' that you are going to key in the next frames. I don't know if I explain myself well, sorry.
I use animation for a lot of things and I have found that it can support many different animations at the same time, at least in my game, which is an isometric rpg, and it is quite loaded.
I trust animation more than tilesets, that gives me problems every day. and the animation lets me copy or modify without problems. but sometimes modifying a tileset is hell on earth