Can't say for 100% ... with my engineering experience, if someone came to me with a problem like yours, I would suspect the power supply.
However, it could be the strip light itself. Maybe it has some substandard LEDs (which are diodes, just like a rectifier), and they're not up to snuff when the higher voltage power comes on from the Magtec. I have seen LEDs do some weird things when driven to the extremes of their operating range.
Can you disconnect the light strip and hook it up to a cig lighter plug in your car / truck... see if it flickers when operating at the higher running voltage from the alternator.