So, I think the odds are very good that the OP is missing something. So, try verifying the gain nobs (are they both the same?). The sends to the busses (are they the same?). Disable all FX using the FX bypass button on the control bar (any difference?).
It's possible that you have found a repeatable bug, but just so extremely unlikely. If I had to guess, I'd think there was some chance you had the focus on a control on one of the busses and spun your scroll wheel trying to navigate to another track. You noticed no change in your GUI, but now your busses didn't match.
Another tip, if you busses are indeed identical and without any FX that introduce random variables, you should be able to flip the phase of one of the two and have them cancel 100% to -inf type silence. If you have FX that generate randomness on the two channels (I think console emulators may introduce this randomness preventing perfect cancellation after the phase flip), then the result of the phase flip will be only the differences. You could then bounce them to a new track and normalize to get a level to hear the difference.