What you need to do is to find the program that is trying to run on startup and remove it. There are 3 places this could be.
First, look in the startup program group. Start -> All Programs -> Startup. If it's there, simply delete it.
Second, if it's not int he startup group, Start -> Run -> msconfig
Click on the startup tab and remove whichever app is bothering you.
Lastly, if it's not there, it could be in the startup registry key. First off, I have to warn that editing your registry incorrectly can cause irreversible problems with your computer.
To check this key, go to Start -> Run -> regedit
Navigate to this key
HKey_Local_Machine -> Software -> Microsoft -> Windows -> CurrentVersion -> Run
This key should look similar to what was in the msconfig startup menu. If the program is there remove the string.
If it's still not there, navigate to this key. (Make sure you're logged into the profile that has the annoying popup)
HKey_Current_User -> Software -> Microsoft -> Windows -> CurrentVersion -> Run
Remove the key from there.
If it still can't be found, you've baffled me