Is there a to scale a md5mesh and it's anims? I know scaling bones is a no no, so I tried scaling the verts but that just messed up my rigging. I just want to scale the mesh/bones but not affect the weights or anything like that.
you can scale it when exporting:
-scale [scale amount] Scale up or down your character during export. Example: -scale 2 will double the size of the character. Scaled up from the origin.
It's because the MD5anims are set up for the full size rig. You would need to import the anims on the new scale rig and re-export them, would be my guess. The MD5mesh has the info on how vertices are weighted to a hierarchal skeleton. The MD5anim has the info on where the points of those bones sit in 3d space.
You may need to import the anims and save out the animation info, then reimport the info for the rescaled bones. I believe that's in File/Merge Animation or something.