Hey Torque You've probably read through this page, but if you scroll down to the "$animations" section it will give you some info on aligning animations to the first frame of other animations. Can't say I've tried it, but it sounds like it could work for you since you mentioned that not all of your anims are backwards.
Ok, so I had two animators work on the animations for Juice (one of the characters in our game) and unfortunately one of the animators had the model rotated backwards in max so when we tried to get the animations working in game, half of them were facing the camera, and the other half away from the camera (3rd person…
Create a new character studio layer, Motion Panel->Layers rollout, then select the bip01 and rotate it 180 degrees. After that you can either collapse the layer and "bake" down the animation or just leave it. That should hopefully fix your problem.
Tried that already. It causes the mesh to fall of the rig and the entire thing gets twisted into a giant pile of crap. I'm more hoping that someone with some HL2 QC file knowledge will be able to tell me a proper QC command to rotate the animation in engine.