It appears that the windows are linked incorrectly to the tab's therefore creating a new window just referenced the bugged tab instead of creating a true new window we needed a new tab and new window together to fix this..
The fix for this was as follows.
in the window that will not retain it's filter settings create a new tab in the window untill you recieve a name like tab 13 you will know it's a fresh tab instance because all check boxes in the filter will be checked. When you reach this pristine tab whatever number it may be re-move all other tabs. then set the filter as you like and repeat for the other windows..
hope this works for you all...
