I've got 1750 miles on my Fusin kit and 2200 miles and another kit and I've never seen your problem.
What battery do you have? C-rating is the amount of power that can be drawn from a battery. Maybe it's too low and shutting the controller down. It should only show itself during load. Test the voltage of the battery when running if possible if if goes below 44v under load then I believe the controller will cut off. The cutoff voltage was set high in these controllers to protect the battery I believe.
Check all connections. One loose one will throw the whole thing off. Sounds like you done this already but check again.
Look if all else fails the guys on this forumhttp://www.endless-sphere.com/forums/ discuss only electric bikes and some of them are electrical engineers.
Don't give up

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