NIOS C compilation and optimization issue

Perhaps you are calling the function with compile-time known constants - so the compiler is optimising away a lot of the code.

If the function isn't 'static' that shouldn't happen.

Or pass the parameters from statically initialised global variables - which the compiler can't know aren't changed before the call.

There is also the possibility that the compiler optimisations are enabled for one file, but not the other - unlikely if you are rebuilding these with the IDE.

If all else fails you'll need to look at the object code - that tends to show up what is actually happenning.