Looks like the SPI has problems as soon as the "slave" tries to send stuff back.
No clue why this happens.
I used 2 simulated atmega328 connected through SPI to each other (1 slave and 1 master).

See the source here:
https://gist.github.com/TheCrazyT/9dc3e6dd31230b493ccf9b2e39fb5215

Download the full source here (with makefiles ... you might need to install arduino-mk):
https://www.dropbox.com/s/0ugmv6uzzkel6bz/board_test.tgz?dl=0
(run make in the "sim" folder and then "SIMAVR_UART_XTERM=1 ./obj-x86_64-linux-gnu/sim.elf")

I currently disabled the lines that produce problems, so you will see one window outputting "A".
As soon as you enable one of the disabled lines it won't show this behaviour anymore.

PS:
Another problem that appeared is that one Terminal window seems to be empty and the output goes directly to the console.