I know that any kind of VNC-type program is seen as malicious by virus scanners. So when I connect my Droid to my PC, Avira Antivir and MS Security Essentials go crazy.
I can live (almost) with the constant notifications, but I've had problems in the past with MSE deleting "threats" even after I told it to leave it alone.
Also, no matter how many times I check the box in Avira that says "Do this every time" it ignores me and keeps popping up.
Oh crap, as I type this it's popping up now, and my phone isn't connected !