Problems of this nature tend to be caused by malware of one kind or another. If you have not already, I would highly recommend running a scan (malware and virus), additionally I believe it would be beneficial to run a scan with a program called Hijackthis. A quick Google search will provide a link for download. From there, you can paste your results to hijackthis.de and you will be given a formatted version of your results with a detailed analysis of each entry.
From my experience, the steps above should more than likely solve your problem. In the event your problem persists, please take a screen-shot of the pop-up (Prt Scr button) and if you could provide more information (operating system, browser being used, and under what conditions doe sthe popup present itself)
Wish you the best of luck with resolving this matter mate. Take comfort in knowing generally speaking, we have all been in your situation and have come out the other side pop-up free. - Rube