For 3 different mapsets, I finally managed to alter them so that, the maps in each mapset could be selected individually, both visible, neither visible or both visible.
Firstly I had 2 maps generated by gpx2img [Only registered and activated users can see links. ]. These are transparent maps. For these I used GMapTool [Only registered and activated users can see links. ] and changed the map name and map ID.
I had both 10m and 5m transparent contour maps from Contours Australia. [Only registered and activated users can see links. ] and [Only registered and activated users can see links. ] . These maps had the same PID and a FID of 0. For these I had to use GMapTool to split one of the img into maps (not "files for Mapsource", but "single maps") and then join all these maps giving a mapset name and new FID/PID numbers in gmaptool join options.
Similarly I used the same approach to alter one of the maps I was using from the Shonky Topo maps [Only registered and activated users can see links. ] and [Only registered and activated users can see links. ]
In the end I managed to make the various maps individually selectable, but I could not have done it without help from people on the forum [Only registered and activated users can see links. ]
Thanks to all. I have cross posted this, to ensure everyone who is interested sees it.
Chris
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