I just found out, that you can actually stop Flash Player from loading "floating Flash ads", by editing Flash Player own settings. Here's how to do it:
Flash Player settings are stored in to .sol file, so you need an .sol Editor to view/modify those settings. After you have installed it, go to following path; C:\Documents and Settings\<user>\Application Data\Macromedia\Flash Player\macromedia.com\support\flashplayer\sys\. Double click settings.sol to open it with .sol Editor. Go to windowlessDisable and check the 'Value' option. Then go to 'File' menu and select "Save".
I tested it and it works with IE, but Opera does not obey that setting. Don't know about Firefox...
I haven't because I use Adblock Plus with Firefox.
I only replied here because for the Flash Player settings to be retained you'll have to untick Adobe Flash Player in CCleaner in "Cleaner->Applications->Multimedia", otherwise CCleaner will wipe out the settings and any modifications.