Linux fails to communicate

Are you uploading one of the time-limited linux "sof" files? If you are then there might be a dialog box that you're accidently dismissing when you shouldn't be.

When you upload a time-limited "sof" file through Quartus Programmer, a dialog box appears that says:

"Click Cancel to stop using OpenCore Plus IP"

When you click cancel, it'll stop the core that's running on your board. By the time you start nios2-terminal, there may have been data stored up in the jtag uart buffer (which is what you're seeing) but nothing else comes out because the core stopped running as soon as the cancel button was clicked.

That may explain the results you're currently getting.