Hi hansibull,
Hope I'm not bothering you (as you mentioned you are in vacation).
Tried miniCore using 16Mhz external osscilator (standard Arduino Uno configuration) and it doesn't work if I compile it as an miniCore; it does work if I compile it as an Arduino Uno board.
I added SPI start transmission and end transmission before and after every SPI transmissiono (or after every group of transmission if I send multiple bytes) and it still doesn't work as a miniCore.
Tried V2.0.1 as well and it behave the same.
I posted a video here - which also contains the sketch I used in the description: - YouTube
The sketch is the complete firmware (not the trimmed down one) and is because the trimmed down one, if I do pretty much any changes it starts to work... however, in the complete firmware I did put SPI end transmission everywhere it should be.
I must say your suggestions sounded like clever things to try.
Regarding programming, if I use the Arduino Uno with standard fuses (16Mhz external osscilator) I can program it in Arduino, no problems (both as Uno and as miniCore). The programming issues I have are if I select a different click and fuses and may be because of some lack of understanding some things. I don't know how to change fuses in Arduino and found that Atmel Ice + Atmel Studio seems to work fairly ok to programm the Uno (both fuses and program memory).
Marius