So trying to help someone out I found a very odd error with SMD importing (In goldsrc model) where BST would flip the bone position of the head, pelvis, and left&right feet. When imported the mesh looked fine but the bones were wrong so when i exported the animation was flipped.

I took the reference SMD and imported it with 3 other 3D SMD editors and did not have this issue. I then re-exported the reference SMD with 3dsmax and when I imported into BST, it imported correctly. Im assuming its something to do with how the original SMD was formatted that possibly had something on those bones that made it invert on import.

This is what an imported animation looks like on the original SMD (broken ref import):
http://www.the303.org/stuff/BST_refanimbroken.PNG

Attached I have the original SMD that fails to import into BST called "Original_ref". There is a regular animation to test with to see how its broken on the ref. There is a second SMD which is the re-export from max which imports into BST fine and with that the test animation works with it on import:
www.the303.org/stuff/BST_smd_importing_error.rar