I just checked in changes to the FlexJS install script to perform checksums on the downloads. You will need a nightly build of the installer to run it, or just use Ant.
The Installer has been upgraded to report more information on each failure. I'm not quite sure we have the right information in all cases, but hopefully we'll get a better clue as to why we're seeing so many failures after we roll out this installer. Note that the new checkums result in a major increase in the total time to install an SDK. The ActionScript MD5 code is significantly slower than the Java version in Ant. This could become our new barrier to entry. I will look into optimizing it, but other folks are welcome to take a shot at it too. Thanks, -Alex