I posted this in the Forum Help in the Popunders thread and am crossposting here since it may resolve a lot of the current problems people are having:
A couple of days ago I got an automatic Windows Update notice that was a security patch for Adobe Flash (Macromedia) because a flaw allowed the takeover of the computer to display the popunders you describe. The notes on the Windows patch also point to a security update on Adobe's site for a version 9.0 of Adobe Flash that is supposed to also take care of the problem.
I installed both and also disabled Active-X and the running of unsigned scripts and have not had anymore problems with popunders or the numerous McAfee virus warnings for a JS/noclose virus that appeared every time I opened multiple A2K screens to read several threads at the same time.
I too have gone through all the exercises of Hijack This, three or four different anti-spyware scans and online virus scans without success. Oh, I also manually blocked cookies from all the various advertising websites used on A2K that even Spyblaster allowed. That didn't solve the problem until the patch was installed.
Applying those patches and turning off the various scripting is the only thing that has been successful so far. For the first time in months, I've been able to read A2K without having my computer freeze and need rebooting from all the popunders.
Windows Security Update for Flash Player (KB913433)
Security Bulletin from Microsoft:
http://www.microsoft.com/technet/security/bulletin/MS06-020.mspx
Security Bulletin from Adobe:
http://www.adobe.com/devnet/security/security_zone/apsb06-03.html