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i recognized that too in 3dsmax9, exporting X via PANDA or Xport.
but for my use in FFED3D they work even scrambled, when i check the option "matrix" instead of "position/rotation/transform" (in PANDA of course).
still if i reopen them, everything is scrambled (horrible)!
but if you set the pivots right (depending all to hierachy) and checked their alignment, that should not happen,
mostly it's their alignment, cause if you mirror objects (and i think you did as well) the alignment of objects pivots gets mirrored too, movement and placement relatively to world and mirrored object is negative (i.e. let's say in a box center is zero x,y,z, left lower front corner -x,-y,-z, right upper back corner +x,+y,+z, doesn't matter which way around, but in one model or world it has to follow the same rule), i discovered also it's hard to get the alignment back to normal.
as long as you playback the animation sequence on 3dsmax it works well (discreet correction, i think), but when you export to any other format, i.e. old 3ds or X, they don't know how you build up your model and everything is wrong positioned and movement is relaying on pivots position and alignment.

short: you should set pivots of the objects in your model all to center of world and align all pivots to worlds alignment,
then it has to work proper!