luisalba,
I have had a similar problem. I believe it has to do with my trace lengths on my JTAG lines. We have a couple of custom boards now, the last 2 I have interfaced with the USB cable and latest versions of Quartus.
With one of our boards, shorter trace lengths, I have no problems at all. With the other, I run into problems when trying to load large programs into SDRAM. Although, my flash programmer works just fine. I can also write to the FPGA without a hitch, as well as the configuration device. I only have problems loading programs to SDRAM.
For this project try using your old ByteBlasterMV. This is a slower device and works just fine for me.
When you lay out your next board, give those JTAG lines a little more attention.
Doug