I am having the same problem and same error on the logs, except this is not happening for any sample application but the application that I wrote and when I try to Debug or Run it from within the FlashBuilder (with ExtensionBuilder plugin) it fails to load the attach the debug.
Anybody found the reason / solution for the problem? I have a gut feeling it has something to do with the manifest file.
I just fixed the problem on my machine.
What I did:
Run a software update on FlashBuilder, i.e., in FlashBuilder, Help>Software Update. This took a few minutes checking for updates and then updating the software.
What led me to do that:
I retraced my steps and realised last thing I did before the 'Debug as Adobe InDesign Extension' from within FlashBuilder broke on my machine was updating the InDesign CS6 to the latest available version, which probably ended up with different flash/flex versions of InDesign and FlashBuilder. So, performing a software update fixed the debug.