The popup message still shows up for me. It's in the source code of all of the threads I've been to tonight.
What is it you're talking about that's in the code, exactly? I'm looking through it, and not seeing anything unusual. I had a similar problem before on both of my message boards that I run, one just recently...but we also had infected board files, so I had to do a complete reinstall and recache, then weed out what I needed to in the database.
If it's something you feel you should PM me with, that's fine...but I mean, every person with a browser has access to a source code. No big deal, though.
Maybe I can help with a solution.