Browndog you'll still need to deal with the malware itself (as you probably have found out already). These can be tricky buggers to pin down. I used to follow the advice found at geekstogo.com back when Windows was my main operating system. Read the stickies and follow the steps and people will bend over backwards to help (or they used to, at least).
The pop ups he was getting were most likely caused by something like you expereinced but the way it got in is (probably) different. I just wanted to stress that killing the malware is only part of the issue and probably not the most important part.
Anyone who jas Java installed (most consumer systems includes it and many programs require it so will have gotten you to install it if you machine didn't come with it) should update Java regularly.