How pinned tabs currently work:
Window 1: 20 pinned tabs
Window 2: no pinned tabs
If I close Window 2 first and then Window 1, my pinned tabs will be there if I open Firefox again. If I however close Window 1 first, the pinned tabs won't be restored. This happens to me every once in a while and it really is a pain to go into my history and carefully restore the tabs, arrange them the way they were before and then pin them again.
I get the idea behind the current implementation but I believe that Firefox should do one of three things:
By the way: Please don't merge this with Make pinned tabs persist between windows (by default). This is not the same and I frankly disagree with the idea.