What direction is the misalignment in?
If left to right I'd say it's just the axle pivots/bushings doing their own thing but differently because the torque tube is disconnected, as soon as you push it over and reconnect it there is no problem.
But that wouldn't cause a vibration?

Grigg

•1951 GMC 250 in the Project Journals
•1948 Chevrolet 6400 - Detroit Diesel 4-53T - Roadranger 10 speed overdrive - 4 wheel disc brakes
•1952 Chevrolet 3800 pickup
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"First, get a clear notion of what you desire to accomplish, and then in all probability you will succeed in doing it..." -Henry Maudslay-