Firstly - apologies to grgsr whose thread I interrupted, but I think our issues are linked.
I think your suggestion re: building the menu first is the one that works for me. The problem I was having was with the integral SiteAssist menu - I did go to some lengths to ensure that I had taken the focus away from the width field. There seem to be one or two minor glitches with my SA setup; one example being that for text, if I apply a font-size (say 12px) and remove focus, it reverts to 9px. I repeat the process, and it always works the second time.
I created a simple 'site' and removed all the pages except for the home page + one other. During the process, I set the widths of the menu buttons - and clicked forwards and backwards through the wizard to ensure that the values for all given elements were sticking.
The preview in the SA Wizard window always responded well, and showed my changes. I tried various was of saving as presets, making sure the nav div had ample space for accumulated widths, gave preset 'saves' unique names, and tried editing these and rebuilding from scratch under a different site (local & testing). Could not get the menu widths to stick.
I still suspect that it's I who am missing something obvious, but for the life of me I don't know what it is. I can build a menu with CSSMenu Writer, (not in Site Assist) and it works perfectly!