You are observing one of the following scenarios:
* I cannot initialize the dataflash of the AT91SAM9G20-EK under SAMBA. I get the following message: "Script Error on Init. Dataflash, Can't detect unknown device"
* The dataflash of the AT91SAM9G20-EK is correctly initialized and seems to be correctly programmed (no errors during programming). But the comparison between sent and received files fails.

The MCI clock (MCCK) is not disabled by the BootROM at the end of the boot sequence. As the SPI0 clock (SPCK) used by the dataflash and MCCK are multiplexed on the AT91SAM9G20-EK the SPI0 clock could not work correctly. Thus the dataflash could not be initialized and/or programmed correctly in the AT91SAM9G20-EK. So the MCI clock must be disabled by SAMBA GUI before performing the dataflash initialization.
And SAMBA GUI source code must be modified as a consequence.
You have to replace the AT91SAM9G20-EK.tcl file by the one attached in the directory: [Install Directory]\SAM-BA v2.x \lib\AT91SAM9G20-EK\