I recently bought a Cerbuino Bee to try out as an upgrade from the Panda II, and had the same problem discussed here.
Specifically, a new generic Gadgeteer project created in VS 2010 ( C# ) would not go into debug. Neither could other code that I found on the Forum.
I then followed the steps covered by Jockey4her to download a new loader and then the firmware, and now the generic project did go into debug.
However, when I started including my own code to the project, the Cerbuino became unresponsive. This echoes what KiwiSaner reported.
I then repeated the steps to download the loader and the firmware, but now I couldn't load the firmware. The GHI Config tool indicated "loder mode", and rebooting the board as instructed by the tool did not change this. In fact, if I switched to the Firmware tab and then rebooted, the loader was now shown as erased!
After a few more tries, I gave up and sent the board back to GHI. I included printouts of screen captures of the various steps, and asked for either a fix or a refund. If this problem was due to a dumb mistake on my part, so much the better if it gets the problem solved.