I posted this over in S3D's forums a couple of days ago, but I guess someone didn't want to read it, because it isn't there. I'm running Win8.1/64bit S3D, so though it probably is the same in all versions, maybe it isn't.

Try this:
Import a model (something irregular and "blocky" so that you're completely sure of orientation)
Double click the model
Try the Rotational Offsets, X, Y, and Z, one at a time moving each back to zero before trying the next just so that you see that all works as expected.
Now, move the Z-axis Rotation 90 deg and leave it there
and... NOW move X and Y

On my machine both X and Y now move in the same plane, so... If I move X 30 deg and Y -30 deg I end up with the part as though I'd never moved either.

OTOH, if I move Z 90 deg and then SAVE. When I double click the model X and Y move as they should.

Bug? Or is this just the way it is with S3D?