Nios/e prints only in eclipse debug mode on jtag-uart, not in eclipse 'normal' mode

I've found also that the JTAG UART is shaky at least, I've spent my share of time trying to fix what wasnt wrong.

I'd suggest if you are using a board with serial connection to use it instead of the JTAG. I've seen this suggestion posted somewhere else and it saved me tons of time.

I would also suggest using PIO with LEDs to convey some sort of watchdog, that the program is in fact alive and running instead of relying on the JTAG UART output.