DE2-115 UART/RS-232 Issue when Booting from Flash

You might have IP in your project that isn't licensed. These components will only work when the FPGA is loaded via JTAG and the programmer is running when in use. Check the output messages for stuff about evaluation versions of the parts. I think the more advanced NIOS processors are like this. They simply don't operate unless loaded from JTAG. There is some Altera documentation on how all this works, but I don't recall where it is.