So, what is known?
1) SD card with original settings works
2) Current settings do not
I'd say start from scratch. If you get the right result from the original settings, start there and build back towards your current settings. Move in gradual steps while listening to the response. That should allow you to narrow the issue down to something more identifiable. For example, maybe it is when setting a different pad--other than cymbals--that the problem creeps in.
It may be a tedious process, and you may need to start over if you miss the point when it happens, but by doing so you should be able to troubleshoot the problem acutely. If it turns out the problem creeps in at random points of the process, then you have more evidence to suggest the problem is systemic in some other manner.
Are you using a different SDcard when you are performing the check between the two settings profiles?