could it be something set in the GROUP pages? You know, the section where you can set up multitimbral routing and splits and so on? vaguely remember this on my m12, and it was caused by overlapping groups, or was it a rogue group set to OMNI?
Also, hate to be capt. obvious here, but have You tried a full factory reset? back to stock everything with the factory patches is a good way to ensure it's not something hardware-related. I know the M6 can suffer some very odd problems from corrupt patches, maybe You just need a fresh start to clear things up? Obv., back up the patches You have if they are valuable.. (etc.)