Forum Discussion
Unfortunately, I never solved it - I ended up ditching uC/OS-II instead. The future of OS-II/OS-III looks very messy at the moment and it seems like Intel aren't keen to keep the relationship going (I wouldn't blame Intel for this).
I'm using Segger's embOS instead which has a fully functioning port available for NIOS II and works with the latest version of Quartus. It's a 'drop-in' replacement for OS-II (i.e. they've a nice compatibility layer that allows Altera HAL software that can make use of OS features will automatically use embOS). embOS also supports the vectored interrupt controller out of the box which was a huge benefit to me.
The Zephyr Project also appears to support the NIOS2 (specifically a MAX10) but I never got around to evaluating it.