Okay, you've got a transform problem.
First, make sure your animation controllers are all TCB (you'll find this under the Animation tab...the tab has a picture of a wheel rolling). Select the particular mesh that is animated, select the Animation tab (wheel rolling), then you'll see a subtitle called Assign Controller. Click on that, and the window will expand and you'll see 3 entries that say Rotation, Scale, Position. On each one, click, then click the little question mark button above it. A window will come up, allowing selection of TCB. Do that for each of the parameters (Rotation, Scale, Position).
Now, the transform problem. You are going to have to unlink ALL the troubled meshes, then find and run Reset XForm (located in the same place the TW exporter option is at). Save before you Reset XForm each part...sometimes there are strange results. Then make sure your pivot points are in their proper locations (you may have to use the Hierarchy tab to Transform and then move and align your pivot points again), then relink, then you may possibly need to reanimate.
FC