Which programs are mentioned in the updates popup? We might be able to help for the updates for specific programs.

CNET's tracker does provide email notification for updates to various software you may have downloaded from Download.com.. As such, you'll need to visit the download locations for each separate program. OR...you can turn OFF those nagging notifications by clicking on the tiny link at the bottom of the page which speaks of changing your update preferences.

Are those the updates you're referring to?

Hope this helps.