Phil,
I suspect that is the problem. Frame and hinge parts are from two different sets. The original hinge for this frame is quite poor, as a previous owner had taken to it with a grinder to grind off the bolt heads attaching it to the window support frame.
I would not be happy to use that damaged piece as it is, and repair might not be a viable option. On Saturday I will try and find a suitable replacement amongst my parts stores. I think there are another 2 or 3 which may be usable. At very least, the current hinge may be good for the driver side frame.
Just when you think things are going well.................stuff happens

.
Wouldn't it be grand if parts fit well.......................or at all, in some cases like this?
At least the rubber set is ready for installing. I finished these last night, while listening to television.