After a frustrating morning, I have realised that if the .cmp file made by the earlier version (pre 4.xx) is present in the folder of post V4.xx version causes all sorts of problems. This is only a problem when a project made in the earlier version is imported into V 4.xx
I copied the whole folder from a project made using 2013-07-07 BZR 4022 and renamed it New_V4 to play with it whilst retaining the working (production) files.
It seems that after getting as much information as possible from the .cmp file using the BACK button on the menu bar of eschema, the .cmp file needs to be either removed, re-named of deleted. When the netlist is made, all of the component data is used by CvPcb.
Once CvPcb has run in V4.06 the .cmp data is embedded in the netlist. This can be viewed using notepad or notepad++ if you are using windows..
Despite the instructions to use the BACK button, it does nothing if there is no .cmp file and the netlist appears to get updated when the parts are assigned in CvPcb. The BACK button will no longer be needed, but if your cmp file is still there it will over-write the data loaded from the netfile, and no matter what you do the CvPcb file will be wrong when you run it again.
This led to hours of amusement today whilst trying to update a project from the earlier version to V4.06.
Am I correct in my assumptions above?