Description
Due to a problem with the Nios® II Software Build Tools for Eclipse, compiler flags containing an = character are not saved when using the GUI by right clicking on the application project and selecting Properties... > Nios II Application Properties and entering flags using the User Flags text box.
Resolution
If you need to add flags which contain an = character you can add these manually to the Makefile by opening the Makefile for your project and modifying the APP_CFLAGS_USER_FLAGS line.
This problem is due to be fixed in a future version of the Quartus II software.