I have had a similar (not the same) problem with my newly installed Intelliflo 4X160 for 2 months, the problem started immediately. The LED alarm,daily,states that I have a under or over voltage, so the Intelliflo's "turn on" time will vary from a few minutes to 45 minutes. The LED alarm will start anywhere 8PM to 1AM after the pump has turned off. Interestingly enough, for 3 days in a row this month there was no LED alarm, and it turned on exactly at the correct time.
My pool company has replaced the communication cable, and is about to replace the mother board.They are reluctant to replace the drive. They are infering that I have a problem from my meter to the pump.
I've had PGE put a surge dector on my meter for 24 hours, no surges were detected. The pump is direct wired to the breaker with #12 gage wire.
Have had a Pentair tech check it out, he wasn't able to pin point the problem.
Another forum thought the problem could be the communication cable or the drive.
Perhaps your problem could be related to the drive. Long shot.