It would be useful to know what the pop-up says, and how it looks. You could attach a screen shot to a reply. There is form to Add images just below the text box where you compose your post.

When Firefox blocks a popup, usually it will tell you in an infobar just below the toolbars, not in a separate window. If you are getting a separate window, that's probably coming from some other source.

One possible culprit is an out-of-date add-on that isn't fully compatible with the latest version of Firefox. You can update add-ons here:

orange Firefox button or classic Tools menu > Add-ons

Click the "gear" icon and choose Check for Updates.

Any luck?

Do a malware check with some malware scanning programs on the Windows computer.
You need to scan with all programs because each program detects different malware.

Make sure that you update each program to get the latest version of their databases before doing a scan.

• Malwarebytes' Anti-Malware:
  http://www.malwarebytes.org/mbam.php
• SuperAntispyware:
  http://www.superantispyware.com/
• Microsoft Safety Scanner:
  http://www.microsoft.com/security/scanner/en-us/default.aspx
• Windows Defender: Home Page:
  http://www.microsoft.com/windows/products/winfamily/defender/default.mspx
• Spybot Search & Destroy:
  http://www.safer-networking.org/en/index.html
• Kasperky Free Security Scan:
  http://www.kaspersky.com/security-scan

You can also do a check for a rootkit infection with TDSSKiller.

• http://support.kaspersky.com/viruses/solutions?qid=208280684

See also:

• "Spyware on Windows": http://kb.mozillazine.org/Popups_not_blocked