It's possible, but doubtful. The hazard flashers are on a completely different circuit that gets power directly from the fuse panel.
When you say the fan controller checks good, I presume you mean that you see resistance but continuity through the switch as you cycle through the settings? Or do you mean the relay is receiving and passing power? Have you checked to see if you're getting power to the fan switch on the dash? The switch that controls the fan speed.
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Friday, August 14th, 2015 AT 10:41 AM