Problem rebuilding source with new Quartus II

Hello,

I recently inherited a project board which has a Stratix II EP2S30F672 FPGA which is booted from an EPC4QC100.

Project originally compiled under quartus vers 7. Now when the project is compiled under quartus vers 9 it compiles without error but will no longer run on target board. I am using the original project files.

I am using an Altera USB Blaster pod for programming.

I was able to download the .POF file from an old working board from its EPC device. I can program that file into a new board and it works so I know the hardware is good. That file is the same size as a new .POF file I build but they have different data.

I found that the unused pins now default to GND outputs (reading other forum entries) and I fixed that. Are there other things that which changed in the compiler configuration which would affect my design? Any ideas? I am new to FPGA design and there is a lot to absorb. Thanks.