Webcakes shouldn't be bundled with your flash player. What probably happened is you were already infected with the malicious adware and it sent you a fake alert to update your flash player bundling the webcake malware to it.
You may want to try to remove it using the instructions here. While you're at it you should completely remove the old flash player that had webcake bundled in and download the legitimat copy. Follow the installation instructions here.
As for the behavior you're seeing with Chrome, it's expected. Google Chrome comes pre-packaged with it's own version of Flash Player plugin, completely separate from the Flash Player plugin used in IE/FireFox.
Hope this helps.
dandab, thanks for your reply but I had already did all those steps but I followed all your links anyway and redid it all as instructed and the popups returned. I did find that I am actually running IE10 on this computer and I don't know if that makes any difference but I saw somewhere if you were running IE9 to uncheck active X filtering. Mine was unchecked so I checked it and popups are gone and all is good in the universe
You probably got it from one of those fake Flash Player update sites, learn more http://deletemalware.blogspot.com/2013/06/fake-flash-player-update-virus-removal.html
You should also scan your computer with AdwCleaner and Malwarebytes.