I have MS Security Essentials on my desktop, in addition to the usual stuff that I use. The only issue I've ever had with it is that it "sees" a potential win32 trojan in a temporary file that Avast! antivirus produces during a virus scan. Once I set it up to ignore that particular folder, it no longer flags that file (which appears and disappears several times during the scan, but is ultimately deleted by Avast). Apparently, the heuristics in MS security essentials sees the "signature" of a trojan in that particular file.
Actually, you shouldn't be running two AV programs at the same time. You should unistall Avast and just run the MS
MS Security Essentials worked better for me to keep a certain pos trojan off my machine.....My previous program Avira kept allowing it to infect my computer and removal was a pain in thearse