Few simulation problems with Quartus II 7.1 SP1

That's usually do to not driving one of the inputs. For example, if you don't drive the reset line, then the simulation doesn't know what the register is doing, and all the registers become unkown, 'X'. It doesn't have to be a global signal like the reset though. If any input is undriven, then the registers it drives become unkown, and that can quickly propogate unkown values through all the registers in the design.