I’m not sure if anyone else experiences this problem, but in the case of someone experiencing it in the future I’ll share my experience.
While rigging a high poly robot I made, I decided vertex envelopes and auto weight painting were both bad ideas. So I went through and made vertex groups for all the parts of my model, and the corresponding bones. Many of the pieces of the model had a bevel modifier active. What I learned was that the armature, when using only vertex groups, did not want to deform the mesh. If I turned envelopes on, it worked perfectly, but envelopes aren’t very good for robots (metal doesn’t bend that way).
(it’s probably a bug in the bevel modifier, losing the vertex group data or something, I didn’t post a bug report since the account server never gave me my account )
The simple fix - either apply bevel modifier and re-assign your vertex groups, or hide the bevel modifier in object mode. (I have yet to try rendering with the bevel turned on and the mesh deformed, since I’m not completely finished with the rigging, I’ll edit this post when I learn if it works or not) Also if someone could help me with the bug report since like I said, I tried doing a report before and the server never finished my account activation.
(currently running blender 2.5.3 64 windows 7)