Not enough info on your setup to be much help.
Are the TB & spinner are sharing the same USB encoder? (almost sounds like it)
Which happs USB spinner are you talking about? (there were a few different versions)
Is the TB the USB version, or are you going through an optipac/optiwiz?
Do you mean switch the axes, or invert each one? (the latter won't help)
Assuming the spinner has its own encoder, look at the board and see if there are any dipswitches.