Hi Borut,
I finally did get past this problem. Ultimately what I was trying to do was calibrate the DDR3 RAM against the 1.2 GHz Quad core part. I ended up having to go through this interesting procedure with the calibration tool.
First, I put the memory parameters into the DDR3 spreadsheet provided by Freescale.
I used the calibration values from this spreadsheet to seed the DDR3 calibration tool. I then ran the tool and got new calibration values. I took the output of this tool and fed the values back into the inputs of a second run of the tool. I did this several times until I discovered that output values were converging. I then took the converged output values and used them in the u-boot code for calibration and voila, the 4 GB of RAM has worked like a charm since. I hope this helps you.
Thanks,
FM