AV software, to be effective, has to hook into various places deep inside Windoze. Some of these hooks are going to be undocumented and not authorised by Micro$oft.
I give you one example: typical AV software checks every Word doc you open, for (typically macro) viruses. A problem with Norton AV, for years, used to be that if the document was password protected, the AV s/w would wait for you to enter the pwd (otherwise it could not check the document) but the box where you entered the pwd was covered up by something else which the AV s/w put up, something like "checking document for viruses". So you got a deadlock... AV s/w is known for all kinds of weird stuff like that.
It's getting better as the years go by, and as almost everybody moves over to XP and M$ Office (and very little else).
I got fed up with these quirks. Life is too short, unless you get paid for doing this
So far, Kaspersky has been fine.
And yes, on one occassion I had to reformat the whole hard drive, after the damn thing totally trashed it... that was Norton I think.