sw,
If the screen on the pump is blank, when in the Service mode, it is because your pump is not wired correctly. An IntelliFlo should get constant AC power. I suspect that your pump is wired to the Load side of the pump/filter relay, which is incorrect. That said, it should not prevent the pump from running when in Auto.
Since I am out of good ideas, here is another one. If your pump is wired to the load side of the pump filter relay, it could be that the relay is bad and only letting half of the 240 get to the pump. The display and control head appear to run on 120 volts, so it is possible the that control head works, but the pump itself will not.
As a test, with the system in Auto, use a voltmeter and measure the voltage between L1 and L2 right at the pump and make sure you have 240 volts. Only measure between L1 and L2, do not measure to ground as that can give you a false reading.
Thanks,
Jim R.