Board Description and Generate problems

I am trying to design a simple system for my custom board with 18 KBytes of on chip memory and a EPCS Controller to hold my firmware. With the ALtera development board I was able to alter the "small" design and add a EPCS controller. I used the flash programmer from the IDE program to download both the FBGA configuration data and the firmware example program "binary_count". It appeared to work.

However when I tried to develop a system for my customized board with the componets outlined above, I got some serious generate errors. I created a board description with the appropriate information plugged into the FLASH Tab. I even assigned a netlist (so that the system could recognize the appropriate chip I was using) {Later I saw one of the threads that outlined a workaround so that would not have to enter the netlist. I tried this option to designate the target device but I still got my generate problem). I tried editing the class.ptr file but to no avail. I installed service pack 1 but that didn&#39;t help http://forum.niosforum.com/work2/style_emoticons/<#EMO_DIR#>/mad.gif http://forum.niosforum.com/work2/style_emoticons/<#EMO_DIR#>/mad.gif http://forum.niosforum.com/work2/style_emoticons/<#EMO_DIR#>/ohmy.gif . I saw there have been a number of threads written on this topic that raised a similar issue. Did anyone ever find a solution to this problem ? Please if anyone could shed some light on this issue it would be of tremdous help

Note I thought of using the command line tools to prgram the EPCS but I came across the following problem. If I set the target board to "Unspecified Board" then I can generate but when I try to compile n Quartus then I get the following errors for all the ports of my system :-

Error: Port "X" does not exist in macrofunction "Y"

Where X = port names in my instantiation and Y = name of instantiation. However back in SOPC builder when I designate my target board to my customized board with its board description then I get my generate errors back again