Glad you're liking the new version
I'm a bit mystified about the issue you've described. No timing with regards to the status window has changed from the old version. Only thing I can think of it that Dropzone maybe taking keyboard focus when displaying the status window which means the keyboard events goto that window rather than the one you meant.
I will look into that, but meanwhile you could try Cmd-Tabbing to the app you are trying to use after initiating a Dropzone action and see if that fixes it.
Regarding the status window position: you can move it wherever on the screen you want by dragging it around and the position will be remembered. You can also minimize it by double clicking on it - it will pop back up when the action completes.