Is there any other process that could be accessing to the data? maybe some backup or monitoring application?
Maybe the server where you run the DB isn’t powerful enough, or if you have other apps using the same DB maybe those apps are using too many resources and MySQL can’t respond quick enough
It isn’t normal, but if you can’t consistently reproduce the problem and somehow prove that ownCloud is the one causing (not suffering) the locks, I don’t think there is anything to do on ownCloud’s side.
If you still hit the lock timeout with a high number I don’t expect that increasing that number will fix the problem, it will just happen later or maybe less frequently.