I dont think that this is really a S90 port related problem, so maybe you can open a seperate thread for this topic. BTW: Are you sure that the the Eye-Fi card supports parititioning at all? Dont forget that this is not a normal card and the Eye-Fi firmware on the card needs to know on which partition the pictures are (normaly partition 1). If you success to create two partitions, CHDK stores the pictures allways on partition 2, on partition 1 there is only the diskboot.bin. How do you think you can tell the Eye-Fi firmware that parition 2 ist the one with the pictures to transfer, and not partition 1?
I think this maybe the reason why it is not working to partition the card with SDM-Installer, maybe the EyeFi card does not support partitioning for that reason.