This is some bug/feature of linux kernel. At boot time it assigns first nonempty slot as mmcblk0. This means that if you have only card in external slot then the 'first/internal' boot item works. If you have both card slots filled and the one to boot in in the external slot then use the 'second/external' item (not tried but I suppose it will work).

Most probably it is a real bug since when the system is booted naming of the slots is corrected i.e. when you boot from card in external slot named (wrongly) at boot time mmcblk0 the result printed by df is that you booted from mmcblk0p2 and have first FAT partition mounted called mmcblk1p1. But both partitions are on the same card :-) I guess it is just cosmetic issue but maybe it can confuse some parts of the system so the best is to avoid booting from external card when internal slot is empty.