What version of MEP are you using? I had a lot of weird issues with MEP 10 & 11 which I usually fixed with a uninstall/reinstall. A huge hassle, but it put everything right again.
Since I've been using MEP 12 and now MEP 14 most of that hassle was fixed. In fact, MEP 14 is very stable on my Vista PC.
If you are not using MEP 14+, you should consider upgrading, otherwise, try the uninstall - reboot - fresh install hassle.