If you are coupling the nano output shaft rigidly to a live axle, and if the shaft and the axle are supported by two bearings each, then your problem may stem from misalignment (parallel, angular, or both) of the four bearings.
We are using brand new toughbox nanos on our drive train this year, and just recently started trying to drive. We noticed a clicking, and vibration coming from one of the toughbox nano gearboxes. Upon inspection discovered the large gear that meshes with the cim motor drive gear was malformed, one of the teeth was wider than the rest causing binding, and noise, about 30 seconds of running the jag fails and blinks red. We replaced that gear with one from an old toughbox and it works perfectly now.
Take your transmission off and try to turn the wheel by hand, if the resistance is variable (gets very hard or stops entirely at one point) then you probably have a similar issue.
I have seen several posts with similar problems, I am going to try to reply to all of them.