Hello,
according to the AVR Series-0 SPI documentation
the IF is cleared by hardware when executing the corresponding interrupt vector.
After much debugging I had to realize: Nothing is cleared!
Second method "cleared by first reading the SPI.INTFLAGS..." works.
And then a third method works too (found in "Getting started with SPI"): Write 1 to this IF bit position.
Can anybody confirm this? SPI is configured in Master/Normal-Mode using ATMega4808.