Yup, whatever the press is doing to make the change from stock to stock it takes quite a while. This is more noticeable in All Weights mode, but once it makes the change it flies!
As for cycling amongst trays as long as you have the trays set the same it will auto switch. I can have all 4 the same or different it doesn't matter.
An engineer told me it is the fuser cooling for the lighter stock. (5000)