I think I have solved the problem. The main issue seems to have been that I forgot to set the YieldCore interrupt to be low priority, so it was probably executing some times when interrupts were supposed to be masked. I’m also still fine tuning the interrupt enable / mask functions so that probably also had an effect.
I now have all the tests running and passing, except for the Intr Queue test. Hopefully the only thing needed for that one is to struggle with the Xilinx API a bit in order to get the 3 timers running properly.