BSERV-9900 increased the amount of time that commit indexing will wait for commits to arrive. Unfortunately, the timeouts weren't increased on the git commands that find the commits. If commits don't arrive within the timeout, the commit indexer will try to stop the git process. However, the process discovers it's been running/idle for longer than it's configured (default) timeouts and throws an exception. This exception causes a complete rollback of the commit indexing process, which means the next time the process runs it will start from scratch again.

Set the process timeouts to sensible values given the other configured timeouts.