Many people have claimed this, so I used Fiddler to debug the web connection process when running the game with ads showing. This has been verified.
It appears to work by doing some cross-site scripting on one of the ads in the form of a iframe. A cgi file then redirects to two other sites (not Popcap and not of US origin) before initializing Java and installing malware. It's also possible it's using an SWF exploit to do this as well. (Oh, it also redirects to twitter part of the way through, which explains what some users are experiencing)
Luckily, it's injected as part of the ad, so any ad-blocker such as AdBlock for Firefox should prevent this problem from occurring.
To be safe, I'll be off the game for a while and will not pursue anymore high scores for the remainder of the week until they get it fixed. (I am in 3rd for the time being, and 2nd after recently getting a 5m score.)