One possibility is that the tension of the top is pulling an un-reinforced windshield frame back too far and it's interfering with the leading edge of the door's window frame.
In case you have nice paint, look closely at that point before trying to close it again.
If this is the problem, you will have to add some kind of support to the windshield, or loosen up the top.
Do you have a front roll cage? If you do, then it's easy enough to run a support of some kind. You can make your own and the vendors sell them as well.
Good luck. Hope it's that simple. If you had good closure before, I'd hate to see you have to adjust the doors and possibly mess that up. Kind of a pain!
Paul