OK, I realise I am making many edits and now answering my own post but I have narrowed the issue to Keyclones "focus on mouseover" function. If I run Octopus with auto add windows set and use it's focus on mouseover everything is smooth and lovely even when starting the clients with the Commands and Maximiser from Keyclone.

Since I have started everything from Keyclone I should have full functionality (I think?), running a mostly disabled Octopus in the background for mouseover functionality is an acceptable workaround.