fkeel:
I have come to the conclusion that I am beyond help - guess its my own fault for buying them without prior testing. However I needed them fast and they where the only ones my supplier had 25 pieces available at that moment :-/Eventually I will be buying new boards and these will be left to collect dust or maybe I can sell them over e-bay at a loss and with a bad conscience.
The ATmega32u4 based boards take some time to get used to. The startup sequence is a bit more complex and has to be understood to get out of the different error states that can occur. When everything fails you have to basically while compiling the sketch hit the reset at the right time, download the sketch and not bring up the serial monitor too late or too early. It is easy to get frustrated and disturb the start sequence. On top of this the USB connection can be lost and the lock file might not be removed. This gives even more error states to consider.
If you still cannot get used to the boards I would recommend first going to the supplier and then to the manufacturer.
In Cosa I try to hide a lot of the issues with the USB Serial. There is no need for the "while (!Serial);". The startup sequence will handle that. Cosa is an alternative support library for the Arduino and replaces the Arduino/Wiring core.
Cheers!