Nios II Linux v1.4 does not support CycloneII?

We have made 2 custom boards in house so far using NiosII. One uses a Stratix FPGA, and the other uses a CycloneII FPGA (EP2C35672C7). Both interface SDRAM. The Stratix board works perfectly; however, the CycloneII board does not play well with the SDRAM, all kinds of read back errors. This is even after installing the SP1 for Quartus 5.0.

It is possible that the problem lies with the board, and not the FPGA. But everything else on it is working just fine. I'm not saying it will or it wont, but there was some problems with the CycloneII and not with Stratix. Our Stratix board works, and the CycloneII does not.

Doug