First, thanks for getting me to look at my installation of Inkscape, which I transferred from my old Windows User to a new one (which I had to create to overcome problems of Microsoft's creation). I realised that the installed extensions had not been transferred. So that is another task for me !! I loathe Microsoft !

My first thoughts on your problem.
a. Somehow the lines that you think are vectors are bitmaps.
b. Your lines that are missing are on a different layer.

If you can let me have your Inkscape files, I will be able to look in more detail.

Cheers,

Rob