Changing (C)Make isn't enough. You will need to recompile the binaries with gcc, or whatever program you linux guys use :P
The script should receive this value for properly complied binaries:
https://github.com/EQEmu/Server/blob.../version.h#L35
Otherwise, it returns '0'
Are you pressing '3' twice? The first time queues needed updates, and the second actually applies them.