I had the same problem and replaced the intercooler pump and the problem persisted. Saw in the forum where wiring the pump so that it come on when ignition is turned on. Only took a few months with some electrical connectors and pices of wire. Just search the forum and look for intercooler wiring. Good explanation with pictures.

The supercharger works all the time now. I suspect a temperature sensor is the issue. Easier to do the wiring versus changing temperature sensor