<rant>First, I have to vent on how frustrating working with Banners is.  There is no specific topic because it's not a module since it's under that Admin.  Second, is no one else having similar problems?  Banners are increasingly a source of revenue and I'm not sure if someone else has an alternative solution or if they can figure out Banners better than I??  Third, I think a banner solution should be able to handle flash banners more elegantly than the following...</rant>

To answer your question (not that I have the right answer, but I do have an answer) to get a flash banner to work correctly you have to remove the destination URL from the flash module.  Instead you need to embed the banner link (such as http://www.dotnetnuke.com/Admin/Vendors/BannerClickThrough.aspx?BannerId=277&VendorId=92).  You should still place the advertiser's URL within the banner screen, just like normal.  This will allow both your views and your clicks to work correctly.  If you aren't putting the above type of link within the flash you will get a bunch of view but have no visibility to the click-thrus. 

If you don't have a Flash editor or even FLA file there are several inexpensive third-party options that let you make an FLA from the SWF and let you change the URL that's embeded.

Ideally we'll see a solution from someone that automatically inserts a transparent button on top of the Flash banners and the click-thrus will work natively.  No, I'm not voluntering...yet.

Paul