ok, it's an AsRock 775Dual-VSTA motherboard, an E6300 @stock, 1GB Ram, Radeon 9700, and an Audigy 2 (I believe that's all that's relevant). All the drivers for everything are up to date, and I was using Vista x64. The same problem occurs regardless of whether I use the 32-bit or 64-bit version of Vista.
I have however reverted to XP. As annoying as it is for me to use an outdated OS, at least I can get everything working under it.
The AUX connector is a 4-pin (though only 3 wire) connector, like the analog CD audio plug, NOT a line in connector. I could use the line in instead, by bypassing the tv-card directly, but that solution, apart from having inferior quality sound (I don't know why, it just always seems to), sentences me to having the sound coming through my system permanantly while the thing is plugged in. The other thing of note is that there is always noise when the audio is recorded through the onboard sound, perhaps I am picky, but the Audigy always gives me crystal clear sound.
Here is the strange thing though. The entire system is fine under Vista, as long as the sound card isn't installed. They all play nice under XP though. HOWEVER, on TWO other motherboards, that sound card is fine regardless of the operating system. Go figure.