mborden: Thanks for the reply
I hate to say it, but since I was not able to fix the bug at the time, I have since moved to xilinx Zynq :P. It is a shame, because I really liked the Cyclone SOC. The xilinx tools are completely free for the Zynq processor, and the SOCs have similar functionalities... so rather than bang my head against the wall...
The fix you suggested could work; however, I have to say, that I won't be trying it at the moment. I have since then uninstalled all Altera tools due to hard drive space. If I end up coming back to the Cyclone SOC, I will give your suggestion a shot.
Thanks