Well I looked around the system configuration of my PS2 but didn't find anything too complicated with the audio set-up... whatever the problem is I don't think it is with the PS2, probably something to do with the configuration of the theatre system you have. So I would look into that above all else. Sometimes you need to make sure the stereo system is on a certain audio channel before the input goes through (but you probably already know this). Hmm...
You mentioned different colours on the plugs... if the stereo/DVD system you are using is new it might be HDD compatible, which have different colour plugs from the usual audio and video Red/White/and Yellow ones that the old standard sound systems have. And the old plugs do not work with HDD sound systems, so perhaps this is the case.
Whatever is wrong it must be something fairly simple. I'm sorry I couldn't be more helpful. *sigh* Good luck T.
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