Hi Keith, I’ve sent my project over now - hopefully it’s just something I’m missing and not a problem with the software. 
I was referring to the ToC location not being saved with the compile format preset as is the location of the Front and Back Matter but not the ToC.
One of my projects is a book series, and I have multiple books with unique ToC that I need to compile.
I thought I would be able to save a Compile Format Preset for each individual book within the project and save all the data I needed for next time I needed to compile it:
I was worried about the possibility of errors when some of data (ToC, as well as ‘Title’ and ‘Abbreviated Title’ in the meta tab of the compile settings) isn’t saved to the ‘compile format preset’.
As I explain in my forum post here, with help I was able to save most of the settings I needed in the end:
There were only those 3 things that I was worried about, but I’ll just have to try and keep them on my mental checklist each time I compile a different book in my project.
I was suggesting that perhaps the Table of Contents tab could act in some way similar to how the Front and Back Matter works. So, instead of typing the name of the title, we could select our ToC page from a dropdown. This could then be saved with the ‘Compile Format Preset’ as the Front/Back Matter locations are.
Perhaps there could be an ‘automatically generate ToC’ checkbox that would have the ‘ToC title’ text box next to it as default and a dropdown greyed out:
If I unchecked ‘automatically generate ToC’ , the text box would be greyed out and the dropdown to select my own ToC page would become available. That way my selection could be saved with the compile format preset the same way as the Front/Back matter options are:
Obviously, just thinking off the top of my head - I’m sure there are many knock-on effects that I can’t foresee! 
I feel like I’m getting past the first transition hurdles now, and am loving the new features in vsn 3.
Many thanks,
Ian