Basically, when you set the path to the log file, Jira wont create any directories that are required - so you tend to put all the cvs log files in the same directory.

However, the write-lock-file implementation :

final Lock lock = getLock(logFile.getParentFile().getAbsolutePath());

means that the lock-file then becomes global - for all cvs-logs - .... because all log files are in the same directory

You want to:
1) create any directories that are required when saving the log file
2) make the lock-file name contain the log-file name - so that each cvs-log file has its own lock file.... even if they are all in the same directory