Firefox and Thunderbird should be able to run at same time just fine as they do not impact on each other program and Profiles for each by default.

May seem like a silly question but is Firefox 5.0 and Thunderbird 5.0 installed in separate folders ? and using their own Profiles?.

Yes, Firefox and Thunderbird are installed in separate folders and their one profiles. I have found that if I have one or the other program open, I can open the other if I hold the Control key down. I am thinking that the problem has something to do with the Panicware Pop-up stopper, Free edition that I am running on that computer. Any thoughts?

Freddyt55

Can you disable the popup blocker in the Panicware Pop-up stopper and then try running Firefox and Thunderbird at same time?

There is no need for a external popup blocker for Firefox as it has its own good built in popup blocker. I recall cases in past where some external popup blockers caused problems like blocking the Options window even.