Custom board with epcs & cyclone error

Has anyone gotten a custom board to work with epcs 4 and a cyclone yet? I have tried for a week and can't get the cpu or flash programmer to work. It either comes back with an error 6 "Unable to synchronize with target." or when I try to connect with the cpu it says that it can't pause it. I get no software response at all from the cpu. I can program the epcs and the jtag device fine seperately, and the altera code is correct because I can make pins function properly, but the cpu in the niosII is not responsive. If I do a sld info on the jtag port, the ports appear to be there and functional. I suspect this is a software issue, but nobody has been able to help yet.

The hardware connections appear to be fine and the target board was develpoed following the manual. I also tried putting a non used bridge in case that would solve anything.

I can make a custom design and software for the nios developement board and everything works fine, so the base install of the software is fine, it just won't work with a custom board.

Thanks,

Dan