You can store different transpose settings for each slot in a performance. Your problem was probably caused by the fact that the Profiler will only preserve any modifications as long as you either use the Page buttons to switch between the slots or you store the performance. Switching between the slots with the rig switches will reset the value to the one that was originally stored in the rig.
If the Profiler is connected to the Rig Manager the Profiler will be in "edit"mode and all modifications will be preserved no matter if you use the switches or the page buttons. This behaviour is described in the main manual.