First off, thanks for the fast reply!
I have tried MiniCore a couple of days ago (manual installation) and could not upload any sketch at all, but at that time I was also messing around with caps and resistors on the board. So... I will try it again, with my current configuration.
It's very good news that you can reproduce the problem!
The probability is high that I can fix it now.
I will check this later today and let you know.
I strongly assume that Watterott is using this bootloader source code:
I changed the bootloader fuses just because I don't want eeprom to get wiped all the time and because I wanted to make sure that it is no startup timing issue that has to do with the external crystal. (I changed the oscillator settings...)
Actually I installed AVR boards 1.6.207 but the board definition in avrdude was missing. (Maybe I looked at the wrong avrdude.conf, or I'm mixing things up. I can just as well uninstall it, and install it again, to be sure.)