I can't suggest how the popups got onto the 'allowed' list if they haven't been whitelisted by anyone using the computer. Maybe it happened by mistake, or when some other site was visited. I never underestimate the fact that devious things can happen while browsing the Internet.

Since you prefer the Mozilla Suite, my suggestion would be to use Seamonkey instead. This is the Suite developed under another name. It has had a number of fixes and enhancements since the Seamonkey team took the project over. I don't know if that would make a difference to unwanted popup permissions being given but if there was something allowing this in Mozilla 1.7.8, perhaps a fix has been done in Seamonkey.