This is how it will be until further notice. Or until another coder finishes the instance system. It works but its flawed and its still better than no instances so lets just suck it up.
Best advice ^
I've also found if I only have 1 instance going (usually guild) I almost never have issues with it. When I make a few instances related to my guild (not even the same zones) they become more unstable. Either way, I send in 1 sacrificial toon to wake it up