10 thousand warnings is pretty excessive, so that could very well be
causing problems. I just updated[1] the code to add the '!' option to
:ProjectProblems forcing it to show only errors:
:ProjectProblems! " show only errors
:ProjectProblems " show errors and warnings
If you can, try that out and see if it works for you. If you don't
like typing the '!' every time, you can create your own command:
command -nargs=? ProjectErrors ProjectProblems! <args>
[1] https://github.com/ervandew/eclim/commit/6340b1b1dab51d8968e89422e028aca9d7b5d581
--
eric