As a recent Start11 adoptee, this one is a major problem for me too. My main reason for getting Start11 was to split out the individual task bar buttons for each window because I despise the grouped window behavior. Start11 has done that, the windows are now split out on the task bar but the job is only partially done, the right click menu treats it as tho the windows are all still grouped!
Please urgently change the Close menu item to close just the selected window, not ALL windows.
(Sorry, posted in the old thread first by mistake)