Can you do a duplex scan using the fi5220c DS in any program other than your own? If not, you probably found a bug in the DS. I would suggest trying to contact Fujitsu for a solution.
If you can do a duplex scan in some other program it MAY indicate that your program will work if you switch to a memory or file transfer. Very few programs use native transfers so perhaps Fujitsu is not aware that their fi5220c DS has a bug when using native transfers for duplex scans.