Ah nevermind. It comes from the second output on the console. Poo.

480i it is for a while then.
The GameCube has an analog A/V and digital A/V connector, which provide the following:
Analog A/V Out
Composite video
S-Video
RGB (PAL consoles ONLY, not available in NTSC consoles)
Stereo audio
The GameCube ships with a "Stereo A/V Cable" which has composite and stereo audio RCA plugs. Nintendo also makes a S-Video cable which is sold separately. In my experience, original and 3rd-party SNES "Stereo A/V Cable" and S-Video cables work fine with the GameCube. Nintendo also sells an adapter to get RF output from the GameCube, using the analog A/V connector.
Nintendo kept the RGB output intact for PAL GameCubes beacuse most European video hardware supports RGB through the widely-used SCART connector. In North America and Japan, the RGB connection type is not standardized, and 9-pin, 21-pin, 25-pin, and BNC connector interfaces all exist. In Japan the 21-pin type of connector somewhat more prevalent.
Digital A/V Out
Digital video (format unknown)
Digital audio (in Digital Audio Interface (DAI) format, not S/PDIF)
YPbPr / YCbCr component video (via component video cable only)
Analog RGB (via modified component video cable only)
There are no official or 3rd-party cables or adapters to enable RGB or digital audio output from the digital A/V port. Some inventive people have figured out how to modify Nintendo's component video cable for RGB output, and interface a DAI to S/PDIF conversion IC to the digital A/V connector, providing stereo 48KHz sound.
The component video cable has no audio outputs, you'll need to use the "Stereo A/V Cable" (packaged with the GameCube) in conjunction for sound.
The GameCube always boots up in 15KHz mode, and will switch to 31KHz (e.g. 480p, progressive-scan) if the 'B' button is held down during the boot sequence, and if the game supports a progressive scan display too. As far as I know this is only available from the component / RGB video output from the digital A/V port. RGB video from the Analog A/V port of a PAL GameCube is fixed at 15KHz (480i, interlaced) output only.