Well, the game seems to be loading animations only from HKANIM files, so I have totally no idea what is the purpose of animations folder. In most cases it contains the same set of animations as HKANIM file (there are exceptions though), so it feels pretty redundant. I think when working with editor, it's best to always load animations from HKANIM file (unless something goes wrong like with the spore mine).
Program crashing when loading animations from either source, is of course a bug which will be fixed in next version. Feel free to point out any models that cause such problems.