I was using the default Altera drivers (are they thread safe?)...but to be sure I removed them totally and set STDOUT to the JTAG UART. Still no luck, though I don't think it actually stops... I've single stepped through the code and it seems to be sat in a loop waiting for the next task to run, without ever starting one. It grabs a semaphore, looks for any waiting tasks, then releases it. (repeat)
This is odd as like I said before, I'm trying to use the default "Hello uCos" application, so have made no code changes...But it never seems to run the two default tasks.
Perhaps I should start a new project with the minimal hardware, I've had lot's of issue's with the NIOS SBT for Eclipse "cashing" files and leaving projects dirty.