Weird window problem.....not the usual one!!!

[MustBeMad]

Hi Folks,
new here and new to boxster ownership. Just bought a 98 boxster with a gearbox fault, got that sorted and all good. However the windows have a weird fault. Have tried the normal reset as obviously the battery had been disconnected for some time etc. What happens is this:
When you open the roof both windows drop by approx 3 inches. When the roof is fully open the windows will work normally, up and down. To the top and to the bottom. When you then fully close and lock the hood in place, if the windows are closed they will drop again by 3 inches. When the roof is closed they will go down all the way and will come back up but only to that point i.e. 3 inches from the top. If we then disconnect the battery to do another reset the windows will not go all the way to the top but will drop by a further 3 inches! This will continue to happen each time until both windows are all the way down, completely inside the doors. And then they refuse to work at all, will not move. In order for them to be raised again we need to fully open the hood. At which point they will fully raise and lower by operating the switch as normal.
One further thing to mention, when the windows are in their 3 inches from the top state, it is possible to close them by locking the door from outside and holding the key over to raise the windows. However, once you unlock the car and then open the door both windows will drop by 3 inches again.
When the roof is fully open the windows operate absolutely normally, up and down, and will drop and raise by approx 1/4 " when you open and close the door as they should.
Obviously the switches, regulators, and motors are all fine.
Any suggestions?????