I have now discovered the problem and append it here for others. I changed the windows by alt clicking two existing windows (w1+w2)and moving them into another wall. Once that was done I deleted the two originally placed windows. I neglected to notice that clever old archicad had given the newly placed windows new window numbers (w19+20) and when I deleted the originally placed windows it backed up the number system.
The result was two windows in the basement having the same number as two different windows on the second floor. ArchiCad obviously became confused!
In future, when I Alt Click, I will check the parameters more thoroughly.