Flashed NIOS II SOPC not working?

What kind of function do your components implement?

There's only a situation I can think of:

Usually when the design works in Debug/Run mode but not with EPCS boot, you have a problem with memory initialization. Infact, the jtag debugger automatically takes care of loading all the required memory sections, but with standalone mode (epcs boot) this is demanded to the bootloader. I remember a similar case when I had to add ALT_LOAD_SECTION_BY_NAME(memory_name) macros in my application to force loading TC memory which otherwise would have not been initialized.