I ran the Reset All Plugins and Update and it hasn't helped and we are all running SP4, I mistyped.
I have also:
Purged the file – using the tool but also manually
Made sure the most recent service pack is installed
Converted the file back into a normal file by saving a copy out
Copied all the model data from all layers/classes into a new file – the windows are perfectly fine
Deleted all worksheets within the file (window schedules etc) – no change
Checked that there is no glitched geometry far from the origin
The origin is not really far away
Deleted all window elements and then created a new window
Tried the file on other computers for other users and with the same result
The issue is still occuring. Any other ideas?