Can you try verifying the following:
Looking through the register settings, it does not appear that there are differences between the GEL file and what you are programming in your init routine.
- Did you set the Clocks and PLL correctly?
- Can you change the RD_DQS to 0x40 and see if it helps?
- Are you making any access to the DDR before the DDR initialization in your setup?
- What type of errors do you notice when you access the DDR address space? Can you confirm these are READ or WRITE errors?
Regards, Siva