Yes, I've had the motor out and disassembled more than once and an Alfa agent here has also had it apart to check the brushes but neither of us thought that the gearbox could be the problem as it works intermittently. The agent thought it could have been one of the relays as there was a voltage drop at the motor but after swapping relays around, the problem remained.
Going by what others have found in this forum, it sounds like the gearbox is the problem so I will take it apart and have a look for myself. Yesterday I took the actuating arm off, cycled the motor using the manual switches and then put the arm back on so it will be meshing in a different location and this has worked so far. While cycling the motor, it seemed to be working harder at one point so this could be a damaged part of the gear.
The strange part about all this is that the motor was replaced just before I bought the car back in 2007 because of the same problem and the roof has had very little use by myself, unless just the motor was done but I suspect it would come as a complete unit with the gearbox.
So, assuming I will find a damaged gear, do you still have any available and at what price? I live in Nelson, New Zealand.