I've upgraded to BTT v4 and tried the new "Show Window Switcher for Active App" action. When I maximize multiple windows of the same application on a workspace (using Amethyst), BTT doesn't pick up all of them. For example, I open four maximized Finder windows, and only one is visible in the window switcher. As soon as I put these windows side-by-side, they get picked up correctly.
A quick test creating 4 documents with TextEdit shows that 'Untitled 3' is missed when maximised, it appears in the list when at its default size. 'Untitled', 'Untitled 2' and 'Untitled 4' all worked fine either maximised or smaller.
Just created 10 text documents and full screened them with Window Switcher->5 and only 'Untitled 4' and 'Untitled 10' are now showing in the list.
Closed all those and repeated but now only 3, 6 and 8 appear in the list when full screened. If I move any of those slightly then some of the others reappear in the list! I'm afraid it all seems a bit random.