I've just added my two-penneth in the previous thread (Java probs in Comments to SubSim).
The other week when these issues first reared their ugly head I only got one trojan alert and that was after almost a week of other people reporting problems, then today I got the lovely red square that other people reported and are pictured above and the same links to Google's security sites.
I too use Firefox, both 3.6.10 and 4 beta 6, but I stopped using beta 6 after the initial warnings as I use McAfee SiteAdvisor which isn't compatible yet for the beta, and the other day I couldn't get any page with beta 6 at all!
Ho, hum! I'm off to thoroughly scan now
Edit: Scans using McAfee, SuperAntiSpyware and Malwarebytes all came back clean, as expected!