I think it's a driver issue, or maybe a RAM cap within the ROM. Like you, I have a Mac SE with an accelerator (Radius 16 Mhz, with external display support), and like you I have an additional 4MB installed that my SE can't see. However, on my card there are two "jumper" spots on one side (similar to the "master/slave" jumpers on a hard drive), and when I move the jumper, my mac will see the chips on the accelerator, but not on the mother board. I know this because removed the RAM from my motherboard, and not only did it boot, but it showed the full 4MB in the accelerator when I clicked About this Mac. Interestingly, when I moved the jumper back, all I saw was 2MB, even after I switched the chips between the motherboard, and accelerator.
It's been a while since I've cracked open my SE, but as I recall, the jumpers aren't labeled, it's just two little sets of two pins each, sicking up somewhere on the side of the board. Also I've tried sticking a jumper on both sets of pins, and the computer simply defaulted to the "2MB" on the motherboard. Since then, I've left it configured to the RAM on the accelerator, the extra 4MB was put back in the motherboard for safe keeping. I'm really hoping that it's a driver issue, because then all I need to do is find the appropriate driver (haven't found that yet). It would make sense, since it seems unlikely that a card would be developed with RAM capabilities that couldn't be used, but then keep in mind that these accelerators were used on the SE/30 as well, so that feature might only be for them. Unfortunately, if it is a ROM issue, then there may be nothing we can do. In any case, I hope this little rant helped, because like you, I would really like to know the answer.
