Could it be possible that you have a portion of your checked out copy points to multiple repositories, one of them not responding? (A particular sub-folder may be causing the issue whereas most of the tool works, for example). This could happen in a corrupted checked out folder or if you use svn externals.
You could also run StatSVN with the -debug command line parameter and see exactly what command StatSVN is trying to execute before this exception and replicate it at the command prompt.
Finally, if this happens after a certain period of time when running StatSVN (after a few hundred diffs), I would try the -threads 1 command line parameter. The server is possibly blocking you because it thinks you are a denial of service attack.
Thanks,
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