You don't happen to be using the Milkshape exporter, do you? If you are, it's the exporter that's the problem: it exports static objects correctly, but reverses the Z axis when exporting animated meshes, so things are never facing the right way -- and god forbid you try to 'fix' it; you'll only make the problem worse, and you'll get some really evil looking results if you try.
Only solution I've found is to ditch the MS3D .b3d exporter entirely and bring the .ms3d into something like Ultimate Unwrap to export to .b3d instead.
Only solution I've found is to ditch the MS3D .b3d exporter entirely and bring the .ms3d into something like Ultimate Unwrap to export to .b3d instead.