It looks a lot as though JIRA 3.1.1 is refetching and parsing the CVS log on every request. While the CVS operation is proceeding, the invoking thread blocks, and other requests queue up (presumably triggering another parse when they complete).

This can be seen by watching the log file on the server. It will be stable when no requests are being processed, will immediately truncate to 0 bytes when a request comes in. Attached is a thread dump of the subsequent CVS parse.