I don't understand how anyone can use vanilla NERDTree because of exactly this problem. It just doesn't feel like a normal or sane editing experience when the tree keeps appearing and disappearing as you switch tabs! It's the primary reason I left Vim for an IDE at one point.

Fortunately, there's a remedy for this (which should really be default in the Janus distro). A simple plugin that makes sure NERDTree is always present and always in the same state across all tabs. https://github.com/jistr/vim-nerdtree-tabs