Are you changing between layoutsin the same file, or between windoes in teh same file, or between windows in different files? What happens when you include the Freeze Window step (it always works for me, but I rarely use multiple windows). If you are going from script to script I suspect the Freeze Window step may unfreeze at the end of each script.
Changing between layouts in the same file.
Your comments about the effect of going from script to script got me thinking about what happens when a layout becomes active. I had set-up a script trigger to run when the layout was entered to Set Window Size. This was forcing resizing of each window as the layout became active which apparently causes the Freeze Window to be overriden due to the the Set Window Size script being separate from the Import File script that is driving.
Turning off the script trigger resolved the problem.