man I had the same crap happen to me.. when I was running Folding as a service a while back.. I had to download the newest version.. and install it to a different DIR. and then not run it as a service any more.. its the strangest thing I've ever seens..I never posted about it.. b/c I didn't know how to say what it was doing right.. and get ppl to understand haha..
but try getting the latest version.. isntalling it to a different folder.. and see if that helps.