I did have this issue once, If I remember, it was related to some conflict with one of my page classes or dataobjects in version 2.3.2. Is that the version you are using? If so, upgrading to at least 2.3.3 seemed to fix it for me.
Hmm, are you capturing any custom data that might ne be properly sanitised by any chance? Maybe people are pasting stuff in from word that contains unsupported characters that is causing issues with the database? Just a thought, thought I can't see how this could happen through the cms.
It shouldn't matter what the application is doing: it is the database that is responsible for keeping the tables sane. My money would be on an update to MySQL to fix this problem. Perhaps the MySQL daemon is crashing or running out of memory? Check its logs.