Many thanks to Vlad the Inhaler for running diagnostics on the site to turn up a few hit counters I missed. I'm not sure if it was an actual virus or just Avast over-reacting to the hit counter. Either way, it should be taken care of.
I will probably be putting up some new -- and different -- hit counters on the main page and the current story page, possibly next week, in order to give this hassle a little time to settle down.