What blocker are you using? Contact its support.

You may have ad / mal-ware. Further information can be found in the Troubleshoot Firefox issues caused by malware article.

Run most or all of the listed malware scanners. Each works differently. If one program misses something, another may pick it up.

I am using the built-in pop up blocker for Firefox. This 'IS' its support.

The built-in pop-up seems to work fine for me, I am seeing no change in Firefox 48.0.1 from any earlier version.

I suspect that you may have picked up a dose of Malware that is causing those pop-ups.

Sometimes a problem with Firefox may be a result of malware installed on your computer, that you may not be aware of.

You can try these free programs to scan for malware, which work with your existing antivirus software:

• Microsoft Safety Scanner
• MalwareBytes' Anti-Malware
• Anti-Rootkit Utility - TDSSKiller
• AdwCleaner (for more info, see this alternate AdwCleaner download page)
• Hitman Pro
• ESET Online Scanner

Microsoft Security Essentials is a good permanent antivirus for Windows 7/Vista if you don't already have one. Windows 8/10 have antivirus protection built-in.

Further information can be found in the Troubleshoot Firefox issues caused by malware article.

Did this fix your problems? Please report back to us!

I have this issue also and now on 49.0 Both on my Mac and PC No malware at all.

Krammig what blocker are you using? Is it compatible to your current Firefox?

FredMcD said

Krammig what blocker are you using? Is it compatible to your current Firefox?

LovePS said

I am using the built-in pop up blocker for Firefox. This 'IS' its support.

Note the Popup blocker in Firefox is not a ad blocker.

This does sound like some adware on computer or there has been cases where some extensions can have a popup in a new Extension update, though this are not normally a big issue out side of open a tab or two. Some proxies may perhaps insert ads?