They seem to move just the way the move in Milkshape for me.What are you using to import your models into FPSC?
By that I mean are you using an entity making program to make your models FPSC ready?
You might look at the .fpe file.
If you are making a weapon the animations for the weapon need to be placed in the same spot as the numbers for the animation in the gunspec file...
For instance if your gunspec file says "fire = 51,60" then the firing animation for that weapon would have to be within those numbers.
I hope this helps.