Better late to a thread than never, I guess......

I assume you've uninstalled the version of Xvid which comes with AutoGK and installed a different version? That's generally not a good thing if you want to continue using AutoGK.

If it's selecting a mobile profile then it's selecting the wrong profile due to you having a different version of Xvid installed. A mobile profile will use more restricted VBV settings (buffer, maximum bitrate etc) and probably cause issues with AutoGK hitting a desired file size in two pass mode, although Xvid can only control the VBV settings when running 2 passes. If you're only running single pass encodes, then using the mobile profile mightn't matter too much.

If you don't use either of the hardware compatibility options, AutoGK should use an unrestricted profile and a custom matrix. If you use a hardware compatibility option, it should use one of the Home Theater profiles. MTK will have AutoGK using a custom matrix, while ESS will have it using either the h263 or mpeg matrix, depending on the compression test result.

Which Xvid settings are you manually configuring which are better than the settings AutGK uses?