Do other cards work in the top slot? I don't mean if they just get power and are seen in ASP, I mean actually function.

I know in my PowerBook G3 Series Rev 2 that while my WPC54G v3 and macally FireWire cards are fully functional in the bottom slot, if I put either in the top slot it gets power and is seen as what it is but they do not properly function.

As to what is happening I don't think I can help you there and would like to know what is going on myself.