if you have an internal server error without take away any file, it will probably an a hosting problem, because of your server (normally shared) it's getting overload
On dreamhost, the same thing happened, what i did its to activate a crontrigger and the garbbagecollector, the problem suddenly dissapear. But i think it was because i submitted a tiket to my hosting company
Excuse my english, but i'm not from US
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