Make sure your com_hunkmegs is setting correctly from the console. Load Gen to the main menu, then type /com_hunkmegs and make sure it reports the proper amount. It should automatically set to a minimum of 128, I built that into .99f's UI system. If that's ok, check your Gen and Quake III Arena versions and make sure it's .99f for Gen, and 1.32 for Quake 3. Also, make sure you're not setting com_hunkmegs higher than 3/4 of your total system ram, and if you're setting it higher than 256, try lowering it to 192 or something like that. I know with my own system it does not like a value higher than 256.
If it's not reporting the right com_hunkmegs from inside the console, let us know. Also, let us know if you're using a loading program like Gamespy Arcade or The All-Seeing Eye. Normally there shouldn't be a problem, but sometimes they load alternate config files and the setting might get ignored in the process.
You might also try enabling compressed textures from the video menu. This usually helps solve a lot of problems, results in better framerates, and should not adversely affect the visual quality of the gameplay. If I could make it enable by default I would, but the setting is built into the executable and forcing it isn't a good idea if someone's card can't support it.
Let us know what you try and if it works, and we'll do what we can to get you going.
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