NiosII printf() not printing correctly

In addition to the suggestions about your 2nd processor, does your BSP include any custom HAL components (or, misconfigured vendor-supplied components) whose initialization functions might be causing memory corruption prior to execution of your main() ?

For example, a table initialization that overruns it's boundaries might go undetected with the "small" library, but now with the "large" library it is clobbering something important, and your printf() failure is simply the first symptom you are noticing.