I tried to compile the latest CDC BootLoader for my Pro Micro(well not a leo but a 32u4) and it turn out that i cannot reupload sketches to the board. The Arduino software tries to touch the Serial at 1200 and tries to reupload the Code. But its not working:

Connecting to programmer: .avrdude: Send: . [1b] 
avrdude: Send: S [53] 
avrdude: ser_recv(): programmer is not responding
avrdude: butterfly_recv(): programmer is not responding
Problem uploading to board.  See http://www.arduino.cc/en/Guide/Troubleshooting#upload for suggestions.

With the older Pro Micro source (recompiled with the older Lufa) its working fine.
I am trying to figure out why this happens.

I also have a similar problem with my HoodLoader2 project. After a serial touch the leds start flickering, usb is detached but no sketch and no bootloader starts. Just the leds are flickering. I am wondering if i set the Watchdog timer wrong in my source.

Any Idea?