It could be the JAVA Heap setting to low for the number of projects you have active and how much activity they have.
You can check the JAVA activity anytime you want with the ''debug'' page:
There are various ''housekeeping'' activities going on all the time and sometimes, it gets bogged down with too much happening.
This can be alleviated by de-activating unused projects, and by adding RAM to the Server and allocating more HEAP (up to 80% of RAM).
We also assume this to be a dedicated server... as in NO other production tools running on SAME server -- these other tools could tax the CPU or use up RAM.