I'm paranoid even of AdwareMedic! It is now a part of a for-profit group and will probably cease being donation-ware sooner rather than later. Keep a copy of the original app if you make an update to the new owners version.
I had one of these pop-up, stuck in an endless loop scenarios a couple of weeks ago. Force Quit, Restart was all it took, but it was very irritating and I was worried I'd managed to download something. I had been making changes to a web site I'm working on and assumed it was something I'd done in php. First few times it was simply going to my hosting provider's error page, then came the pop-ups. Not sure they were not being hacked for a time, either!
At any rate, AdwareMedic has never found anything I've run it.
I think I still have a copy of ClamXav around... (...which is also now a commercial app. At least the original dev is still the lead dev.)