ok, some points you may want to check:
* make sure your CPU reset vector (and exception vector) points to the right memory
* your software will run, by default, in the biggest memory connected to your CPU. You can change that in the BSP Editor.
* stdout must be correctly set to your jtag uart device in the BSP Editor
* check for timing issues, it may cause your system to malfunction (or "no function" at all). Big on-chip memories will make it harder to route and may cause timing closure issues.
* you may want to debug your software using Eclipse debug capabilities and run it step by step so you will know where and what it's going wrong (debug as -> niosII hw)