Problem Running Nios II Design Standalone

It's working now! I figured out how to remove the dependency on the JTAG UART in the Eclipse project, so that peripheral is officially out of the design like you suggested. The design has been free-running for several minutes without an issue.

In case it is useful information to anyone else, I removed the dependency by right clicking the BSP project in Project Explorer, then selecting Nios II > BSP Editor. In the Main tab, under Settings > Common, I had to change stderr, stdin, and stdout to "none."

Thanks a lot. Figuring out that it was an issue with the JTAG UART is the sort of thing that would've taken forever to find on my own.