Don't set numHelperThreads to 1.
If you set numHelperThreads to 1, any slow task will trigger an APPARENT DEADLOCK. c3p0 relies on an internal Thread pool. One thread does not make a pool. Let numHelperThreads have at least its default value of 3.
Specifically what is going on in your stack trace is that an attempt by the Connection pool to close() a Connection is taking long time, for some reason. There could be a real problem here, if this happens a lot, but it could just be an occasional slow operation, which a reasonably sized Thread pool would just handle and shrug off.
Good luck!