I may have a solution to your problem and it deals with the "first joint" deal. I dont think its a milkshape vs max export thing but check this out. Maybe give this a try.
*On the frames where the model is dodging drop the first joint or "root bone" to half of the height of the character.
If you start with the standard FPSC skeleton then this will not affect the position of the model as is, so you will have to find the first bone that is accually connected to the model and drop it the same distance. This may possibly make FPSC read the top of the character as half way for these frames given the point of the Y axis (wich in past versions was read rather than the piont of the root bone). The only delema is how can this be done without moving the rootbone for all the animations. I have not tried this yet but I may give it a shot soon. You may have to start with a completely blanked animation skeleton and create all the animations yourself to achive this if the rootbone can't be moved within the animation frames. That's just my 2 cents
Hope it works out.
This kind lends to Rolfy's input.
EDIT-Should you wan't no damage to the player maybe dropping the rootbone to the full height of the character may work.
EDIT part2 The revenge-It can't be done in Fragmotion. All it does is move the rootbone for ALL frames of animation. Perhaps if you havd a custom skeleton with the rootbone being attched to the pelvis bone it may work.
I think it's on the right track, it's just how to execute it is the problem.