I've already started this and found some diffenerces but to no effect on the final display yet - I'll obviously have to check more diligently.
What are SSL settings?
Is anything retained in computer memory when the help is closed (e.g. the last search) and can this be cleared out?
Single Source Layout - those recipes that generate the component parts of your final help project
Thanks again Colum, I have indeed been careless in the past when selecting the buttons for the window. However this wasn't the prime cause.
David Hutchinson of the ISTC in the UK told me the cure -
"Check the section in the project's HHP file - open it in Notepad. The problem is likely to be that each line for a merged file includes the path to its folder. Remove the path and recompile the chm file."
The files that worked were just listed plain, those that caused problems had the file path attached.
Paths removed, problem solved.