Hi,
Make sure to update all the timing values, page size, row,col size in ddr_defs.h. Best bet would be to try JTAG emulator. In CCS, TI provides gel script to R/W the DDR3. You can even find out stuck bits in data lines.
http://processors.wiki.ti.com/index.php/AM335x_EMIF_Configuration_tips
Thanks
siva.