Hi, some questions to get you moving:
Have you updated your pedal? There is new software available that fixes a bug we found after we shipped the first batch of Blackholes where something similar could happen on some units. You'll need to plug in the USB to a computer and use Eventide Device Manager to update to the newest version (1.0.1[0]).
Are you using the included power supply? This could also happen with a power supply that isn't providing enough current to properly feed your Blackhole.