OK, I think I have fixed one of the problems but not the other.

First problem was that the spring had crept past the coil holder and as a result there was a physical issue where the flipper was sticking pretty consistently. This was confirmed by switching the machine off with the flipper stuck and the flipper remaining stuck. When I took the stop off again I realised that the spring was out of position. This issue is now fixed! Manual testing of flipper confirms no physical sticking (plus I tried tapping the bottom of the flipper shaft just in case).

Now, the flipper is sticking due to an electrical or electronic issue. It still gets stuck, but this is definitely due to current flowing through the coil, as when the machine was turned off with the flipper stuck, it dropped back immediately. In fact, when the machine was turned back on the flipper moved to full stroke! I think I will be checking the RHS flipper button/switch for starters, as tapping the cabinet or hitting the button a second time will cause the flipper to drop back down.