If you encounter such issues you might need to take precaution as soon as possible. This seems to be the case of a malware infection. Download GMER and choose random executable when downloading from the official website. This way the malware won't kill the .exe file. Perform a scan and delete everything that is marked with red color.
Then download ComboFix to remove traces of the malware infection that spread through files and registry keys. Don't use the computer while the tool is running and wait for a report. The computer will restart at some point, which is normal, and when the reboot is complete, a LOG file will be generated that contains all the operations from the scanning procedure.
At this point, all pop-ups will be removed and infected processes deleted.