I have finally got to the bottom of this colormap problem. The problem wasn't in the reassignment parent, nor with the GUILayoutToolbox. It was actually to do with preview() of the Image Acquisition Toolbox.
Executing preview() somehow touches all my colormap settings. On screen, my colormaps get set to 'gray'. On save the panels, these images are saved as 'parula'.
Solution: Resetting all my axes to the correct colormap after executing preview() solves the problem.
Blessings
Spencer