X'ing out windows doesn't work when pinned (though right click -> close does); In a multi-tab: sometimes i can't drag individual windows out once multi-tab'd; sometimes it doesn't let me adjust width / height in a new position. Interacting with it could yield others.
Of note is a truly severe issue where you can X out all the windows to an unrecoverable state where opening the debugger just crashes the whole emulator; i had to rebuild the emulator from scratch and wipe all settings to alleviate this.
If you want to play with it yourself: File -> Reset to Default Layout can help you if it gets in a funny state.
I think it just needs a little attention is all. Thanks!

EDIT: Ok, sorry, for my original post i had code from a couple months ago, i've updated and it seems a bit better now, i edited the post and the issues listed still exist (not sure about the one where you X out all the windows, but at this point, i don't wanna try it again...)