Issue
Corresponding threads in some custom CQ Services lock each other because of synchronization.
Solution
Build your CQ Services so that every CQ Service uses its own ticket (and not the system ticket). Overlay rep. own implementation of AbstractService#getServiceTicket(Ticket) and create a separate ticket with the Ticket#duplicate() method.
When using ticket.duplicate(), make sure that such objects are closed (see [1]).
The system ticket itself is initialized at CQ startup, and closed only when CQ closes.
Additional information
This issue occurs when custom CQ Services extend AbstractService and don't overlay AbstractService#getServiceTicket(Ticket) to get a separate ticket. Therefore, the same JCR Session for all CQ Services is used.
[1] http://javadoc.day.com/com/day/cq/contentbus/Ticket.html#close()