It shouldn't be the cause. There have been instances where I haven't done a scan for over 30 days, but I have also disabled the alert for that issue. I don't know if that makes a difference. It shouldn't, but you never know.
It's possible that you're infected. I suggest a full scan with updated definitions. If you don't find anything, you can try scanning with free MBAM and SAS.
Is there perhaps some interaction between Windows Defender and McAfee ? I haven't used Windows Defender since I found out it was a lame program (Windows XP). Do you use Vista or XP ?
Anyway, what version of the SecurityCenter do you use ? In version 9.3 'FIX' supposedly works, but not always in previous versions.
This disabling of real-time scanning, in what kind of situations does it occur ? I think I've seen it with a bad update, but I'm not sure.