I tried to use the Yamagi Quake 2 source port. For whatever reason, the game stays at software mode, even when I try to change it. Can anyone help me?

Check Documents\YamagiQ2\baseq2 for config.cfg. If it's set to read-only, I imagine that would be the problem. If not, perhaps you could try changing the settings in that file manually and see if it makes any difference.