[U-Boot] loading via jtag

Hi All, Has anyone used the JTAG like the BDI2000 to load u-boot onto a at91sam9263? I've done it on other boards but some some reason the code will not execute from on board SDRAM. To avoid initializing the external memory via jtag, I use the bootstrap code to do the setup then load u-boot and run it. For reason(s) I haven't figured out yet, the code will not external memory. Has anyone done this before and can provide some help? Thanks.