Re: Ground loop concerns?
A lot depends on how far apart the two circuits are. If they are only 1 foot apart, why not connect the grounds of the two power supplies together? And make sure you are using heavy gauge wire for each of the pcb-to-power supply connection. You want less than 0.1 V drop along that wire.
A lot of power supplies have 3 terminals on their outputs: + out, - out, and "earth ground". If the - out is your ground potential, sometimes you want to connect it also to the power supply's "earth ground", and sometimes you do not!
If the two circuits are 15 feet away, in different equipment racks, you could easiliy have a 5 volt difference in ground voltages (some combination of AC and DC offset). That is enough to blow out a digital circuit, or at lest compromise its noise immunity.
This IS a fairly common problem, and it is solved by using "line drivers" and "line receivers" that send the digital signals via a shielded twisted pair that is not referenced to board ground. Other methods include opto-isolators for slow signals, or fiberoptic digital connection for very high speed signals.