I've recently noticed the problem, and customers have reported, that websites that use a Flash based file upload control don't work.  The example I have been analyzing today is Magento eCommerce, uploading images into the catalog.  The older HTML style input type=file control works fine of course.

The short story is that the latest vesions of Flash 10 player, embedded into your browsers, essentially broke this, and apparently it has been quite a debacle.  While some web application developers have updated their software to work around it, not everything has been updated, and sometimes upgrading a webapp on a production server takes significant time and can't be done quickly just to resolve one issue.

A workaround I have verified, for Magento at least, is to uninstall the Flash Player 10 from Add/Remove programs, and then install this one:

http://haveabyte.com/flash9.msi

Here is the IE version:

http://haveabyte.com/install_flash_player_active_x.exe

This is version 9.0.124.0 and it solves the problem for Magento (tested with version 1.1.6.). I apologize that I didn't keep the original URL I downloaded this from, but I'm pretty sure it was from a direct Adobe URL, posted by someone into a Magento forum thread, and it has been scanned with the latest versions of Avast and Spybot S&D (and I'm running it so that should tell you it's safe.)

I hope this is helpful.