I Updated yesterday from an early release of Windows 7 to the retail release doing a complete wipe of my computer. After installing Flex Builder 3 I tried to do some work, yet every time I launched the program Windows 7 alerted me that I was running a program with an unknown publisher. After hitting my self in the head I released that unlike my regular Eclipse environment, Flex Builder was not using my VM but the one that is packaged. This packaged version is NOT signed.

For some reason this worked fine before; but now, not so much. Setting the [-vm c:\pathto\javaw.exe] in the eclipse.ini did not work, but changing the shortcut did work. Any insite into this is welcome!

So in short, on windows 7, force your VM to a legit installed JRE to get this pop-up message to go away if your getting it! The packaged one is not in favor with Windows 7 security!