messed up exported animations

I am truly new to blender. I’ve spent the last month trying to get a handle on it and have been successful making and animating and exporting several models. I export to iqe (inter-quake model format) and use the models in a version of cube-2 game engine. All that said, I have some models that animate fine in blender, but when I export and try to use them they appear as if they’ve gone through a broken transporter (startrek…). I’ve tried every thing I can think of and have looked diligently with google and haven’t found a thing. These models, for the most part, were imported .obj format. They look fine. They have no rigging so I do the rigging and the animation. All are quadruped animals. Blender 2.69a. I have ‘align to view’ on. I do all rigging in front ortho direction, if that matters. Any help would be tremendously appreciated. I’m sure this is a lack of knowledge on my part… Also, I have a wild boar I animated just fine; I do the same with 3 different wolves and no go. Thanks!