Strange Vibration when loaded

You can tell simply by looking at it. A drive shaft being in phase just means that the yokes are aligned. If the slip yoke has been removed its possible to spline it back together with the slip yoke not aligned with yoke at the rear of the shaft which would be out of phase and cause a vibration.

 

In Phase means the shaft at one end the yoke is in the same position, each shaft down the line. One shaft will be 90 degrees from the other. If they are out of phase the drive line wants to straighten out every revolution.
If the drive line is not set properly, the angles it will speed up and slow down twice in a revolution, that will destroy transmissions, it is like a little hammer hit 4 times a revolution.