I have sent a bug report about this to support, since I can still reproduce the bug since the latest OS update.
I've checked this thoroughly and it happens every time. When I switch between different programs with different layer A/B configurations, via SysEx edit buffer dumps, then something is not initializing correctly. When switching from a stacked/split program to one that use only Layer A, then the sound change for every 4 keypresses (I'm on 8voices here... those with 16 might have them switch every 8th keypress, I do not know, or maybe it's only an 8voice bug)... when the program I switch to is one with stackA/B, then one of the layers is not sounding...
Sometimes, if you switch to a program that uses the sequencers, it will run extremely fast, and not per the program Tempo.
Something is not initialized correctly I think, when receiving an edit buffer dump... as soon as you double click either SPlitAB or StackAB buttons, then things get correctly initialized.
Some may say that this is minor, and that there is no problem in just pressing those buttons two times... but when you use a computer editor, that lets you browse programs by sending them to the edit buffer, it really becomes a pain in the neck because every time you select a new preset from a library on your computer and it is send to the edit buffer, you cannot know if the sound is playing the way it should, and the only way to be certain is to double click those A/B buttons... and to have to do this every time you select a new preset in your library is simply extremely irritating.
So I really hope this bug will be fixed... I'll report back if the bug is confirmed by DSI, and if they will add it to the bug fixing list.