The problem is not the filesystem of the cards. There is no problem executing programs from vfat or fat32 partitions. The problem is that the partition is mounted with noexec option, as a "security measure".

If you want to change only for now, use a command such as

mount -o remount,exec /media/mmc1

If you want a permanent solution, see here:

http://www.internettablettalk.com/fo...ead.php?t=9777