Well, another think to try would be disabling JoomSEF cache.
Or, if it gets the problem again, then do not purge URLs, but just clear JoomSEF cache.
There is a possibility, that the file locks do not work as supposed on your system and the cache file get corrupted. This can be then solved by changing the file locking option in JoomSEF configuration or disabling the cache.
However, usually, this problem does not generate 500 error but some other one, commonly a parsing error.
Except this, I have no more ideas. It might be also some kind server specific problem that appears only in combination with JoomSEF and URL rewriting. E.g. the URL generated is conflicting with something on the server and similar.