Fuji,
One clue is that you mention you are modifying the "Hello LED" example. This software example is designed in part to show a very minimal (low memory usage) application. As such, several of the software library options are turned off... if this is the case it may be causing the flash problem.
To see if this is the case, right-click your project in the IDE and select 'system library properties' On this screen, ensure that 'small C library' and 'reduced device drivers' are not checked. The Nios II software developer handbook should discuss what these options do... but if I remember correctly, they may prevent use of the flash routines to save code-space, if selected.