I use a GC component cable in my setup but I don't have one of those input switch boxes to test it with. However if you think about it why should it matter if you are running through a selector box? Even though the cable is a proprietary it is still just a cable outputting a 480i signal. Any weird Nintendo magic it is doing is being done in the cable so by the time the signal comes out it is 480i. So if it's just a cable spitting out a 480i signal how would the signal tell a difference between being plugged into a T.V. or selector box?
I got sick of switching cables and only had HDMI inputs left on my T.V. so I got a converter box. It does s-video and composite to HDMI. I use it for my Saturn (s-video) and Genesis (composite). I searched for awhile and this was the best one I could find that wasn't way overpriced.
http://www.amazon.com/Composite-S-video-Audio-HDMI-Converter/dp/B003NS0UUQ/ref=sr_1_4?ie=UTF8&qid=1300814494&sr=8-4I am extremely happy with it. You don't really notice any better of a picture but it solved my problem. My T.V. does say the signal is 720 at 60Hz when you run it through the box though.
They have those converters for any input to output combination you want. I just went with that one because it was exactly what I needed and the price was great.