First things first. Do a full virus scan on your system. If you
found any, quarantine it. Reboot when the scannning is finished.
The popup may be caused by a virus/malware.
Try isolating the problem by temporarily disabling third party
programs that are run at startup using AutoRuns.
http://technet.microsoft.com/en-us/sysinternals/bb963902.aspx
In AutoRuns, go to the "Logon" tab and disable all entries whose
programs) except those that are anti-viruses. Then reboot the
system.
If the problem disappears, then it must be caused by one of the
disabled programs. Refine the isolation by enabling the first half
of the previously disabled programs. e.g.: If there were 10
disabled programs, enable the first five. Then reboot. You'll have
to use this method until you find the exact culprit.