If permeate flow rate verses time for both membranes are plotted will there be a difference?

There should be a difference in the plots - at least initially. There is typically a "conditioning" affect that occurs as the result of mechanical compression, some of this affect is reversible to an observable amount if operation is intermittent.

This will yield a "zigzag" appearance to a graph of operation vs. time or cumulative hours of operation. The trend with the intermittent operation would be to gradually approach a standard.