I had some similiar issue.
Problem was that drupal was cosuming 100% of cpu usage, sometimes making the execution of some queries to take to long and reaching the max timeout on LOCK_TIMEOUT
If you have acccess to command line, check proccess, cpu usages, sql usage and so on
Hope it helps
There are some threads about drupal sites cosuming 100% of cpu (Kind of old but i had this problem recently), take a look
See this thread for a bit of debuging