FFTI is likely legit. You use skype, yes? If not, write down what it says in case you need it and then delete it.

Did you check appinits? Also what version of windows are you using exactly?

Is the symptom that you kill the process, delete program, restart the computer, and it's there again?

Check all instances in the registry (local_machine, etc.) where there's a software/microsoft/windows/run* for a reference to this program. Check to make sure it's not something really stupid like the startup section on the start menu.

All popups are IE, right? Did you check to make sure that you don't have any IE add-ons that might be causing it?