I'm not sure what you mean.
If you load with PS.FI2, the size of the card is irrelevant. If you are having trouble running scripts, it is some other problem. If you have set a script to autostart, it should run when you load the FI2.
If you multi-partition a card, then the scripts must be on the main (large) partition, not the small one with diskboot. But sd1100 port does not support multi-partition.
