Righty, you don't specify when popup's appear, so in case they come out even if you donpt have open IE or the browser of your choice, chek the Run key in the Registry, a program may be executing from there.
Key Path:
Start/Run/Regedit
HKLM/SW/Microsoft/Windows/CurrentVersion/Run
From there you´ll see the list of programs that run in your computer after boot time (a brief descritpion is also available). If you see any program you don´t recognize delete that line...... but be very carfull
PS. This is just if popup's appear even if browser is not open, or at least this was the senario I had and worked fine.
Good Luck....
Technically... ¡Everything is possible!
Biohazard