Resurrecting an ancient thread but this happens semi-regularly to me. I'll suddenly realise that multiple, unrelated notes, in different regions, on different tracks, are muted. I can't conceive how it could be me doing it accidentally, because it's so spread out and random. Sometimes it happens on tracks that are frozen, so I only realise there are muted notes when I unfreeze and some notes don't play.
I also have a common issue where notes randomly un-quantize, again affecting random regions all over the shop, so there's no way it could just be an accidental key command.
Finally thought to have a look and see if it's happening to anyone else... lots of abandoned old threads like this one, but no solutions.