The breakout board that I know (the one documented with the Cyclone III c120 development kit) has a serious disadvantage: It hasn't any ground pins at the debug header. I don't think it's particularly suited to connect single-ended high speed signals.
Oh man, that's bogus ... but you are right. Attached is the breakout header schematic that was delivered with the Stratix IV GX development kit.
Perhaps the HSMC to GPIO breakout board would be better then. The original poster can download the schematic for that.