AT91SAM7S256 Header Board, Cannot verify uplloaded binary.

For some reason or another I 'm missing how to upload a binary to the header board with the JTAG 20 pin adapter. Every time I upload a binary it seems that some bytes are written while others are not. When I use the SAM-BA program to write the binary everything “works”. The program does run as I expect it too, but in CrossWorks I can debug the binary. I upload the binary in SAM-BA and then Im able to debug in Crossworks. Has anyone had similar problems? Im trying to get the LCD software for the nockoff nokia running on the sam7 header board.