Originally posted by ZeqMacaw:

This is likely a problem with Crowbar, rather than Blender Source Tools. I am not sure why some bones decompile at weird rotations or how modders fix it. I am more likely to find a fix for the problem if you post a bug report on Crowbar's steam-group Discussions.

Okay, thank you so much! If it helps, when I import the .qc file without any animation, the bones are rotated correctly. However, on importing an animation from SFM, the bones are rotated to weird angles. Also, I figured how to fix it but it requires the animation not using a biped_rig in SFM, which I like to use so this is a downside :(

I made an animation and exported it to a .dmx file and using the Team Fortress 2 Scout Bot model that comes with SFM (converted the .mdl model to .qc with Crowbar), and importing my animation works but some of the bones seem to be rotated 90 degrees upon importing the animation, and it happens to be the legs and the arms. Even if the legs are not animated, everything gets shifted and moved with the bones, and therefore the mesh becomes distorted. The model is rotated 90 degrees to the Z axis (as almost every animation does), but the legs and some other parts of the model are distorted in what seems to be 90 degree increments on the Y. In other words, the animation distorts some of the model. How can I fix this?