For example, when I ran Heaven earlier my GPU clock increased too 1201MHz, yet when I was playing Quake III it stayed at 1006MHz. Yet I had not changed any of the settings in afterburner.
Quake 3 will undoubtedly be CPU-limited. The 'boost' auto-overclock will be a function of current GPU load, as well as current power draw and framerate.
If GPU load is sitting at well below 100%, there is little reason to increase core clockspeed.