I had a vaguely similar issue with productions a long time ago (Worker timeout (Stock Entry/transfer on Production Orders) - #10 by trentmu).
I found that if I just left the screen with the message about the timeout (ie. don’t click Close) for a while (sometimes as much as 3mins) it finished the submit in the background. I never got as far as solving it, but maybe you will get some ideas from the logs etc that I posted there, and can sort out that one too 
I suspect it is just a database problem, as I had not optimised my DB at all. I will get back to it in the next few weeks. Perhaps your system will exibit behaviours that allow a more accurate ID of the problem.