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We've been running with the javac parser for about a week now and we haven't seen the same issue come up again. So the problem is probably that the eclipse parser is very inefficient.
It would be nice, however if a warning could be displayed when configuring the plugin if the eclipse parser is selected (to help others avoid this mistake). It seems reasonable to assume (but correct me if I am wrong) that most Jenkins users are compiling with javac and not eclipse. Maybe a warning like the following could be displayed:
Warning: you have selected the eclipse parser which is known to have performance problems. You probably want to use the javac parser instead (unless you really want to parse output from the eclipse compiler output).
Changing the bug name to reflect this change in focus.