1st question: Do you have an Antivirus s/w installed on your PC..?
2nd: Your AV s/w, is it updated? when was the last scan you made?
Regarding your issue,
1st solution:
Try to boot up your PC in safemode (better on safemode w/ networking and logging in as Adminstrator), run win disk cleanup (cleanmgr.exe in RUN)
after that, if you say YES 1st and 2nd question nako.. Try to scan back again and check if you have this popups or issues again.
2nd solution: Boot pc in Last known good configuration. (thru the windows advance option screen)
check if you have this popups still
3rd solution, fails, try doing a SYSTEM RESTORE on your pc. (in safemode w/ command prompt)
type in the dos prompt: %systemroot%\system32\restore\rstrui.exe
pick a restore point (where everything was a.ok.. a week or 2 weeks ago) and after you have done this check and observe if everything is NOW o.k.
Worst case sceneratio: Format the drive..
Good luck!