There are two major causes that come to mind for this (there may be others as well, these just seem to be the most likely). First would be rotation order, which you've probably thought of. Some discussion of TG2's rotation order here:
http://www.planetside.co.uk/forums/index.php?topic=13730.msg135056#msg135056It is of course critical that the rotation order be the same or be mapped correctly between different systems, and note Matt's last post in that thread on the added challenges of doing with differing coordinate systems:
Quote
It gets even more tricky to keep track of the differences when different programs have a different XYZ system. For example, if the Y axis in one program is equivalent to the Z axis in another, then to match a rotation order of 'ZXY' in the first program you'd need to use a rotation order of 'YXZ' in the second, because Y is really Z.
The other major possibility could be numerical accuracy. If you're working on a scene with very large scales, or working very far away from the coordinate origin, you can run into issues with a lack of precision in position values due either to exporter limitations, or simple numerical limitations.
I don't have any experience with this stuff myself unfortunately, so I probably can't be of tremendous help, but if you can post a sample CHAN/MOV file and some more details about your scene, possibly one of the rendered frames for reference, then hopefully we can resolve it. I'll have Matt take a look at this discussion once there's more info to go on.
Edit: I see you submitted some more details in the support email, so I'll work with Matt on that.
- Oshyan