Have you checked for ground loops ? Is it possible to plug both your amp and all your power supplies into a grounded multi plug or surge protector? This will stop ground loops.

Other common sources of hum are from fluorescent tube lights and computer monitors / TVs. Good guitar shielding / turning monitors off when playing can solve this problem.

Are you using any other boss pedals like say a graphic EQ ?
I had a similar problem with the Boss OD20 and the GE7 eq pedal. The GE7 was fine with an MZ2 metal pedal but as soon as I switched it out and replaced it with the OD20, the OD20 and GE7 produced so much noise that my poor little noise gate couldn't handle it (like my good self).
I solved this problem by selling all my Boss pedals and going Digitech instead !