@Gavin Ross Now I understand your situation. I think your issue is that the two same policies conflict.
There's a link order in GPO. For detailed information, you can refer to this thread and this thread. In short, there's only one GPO can win if you set the same GPO for twice or more.
In your situation, the same GPOs conflict and the first one wins which overriding the others. I think you can try to adjust the GPO's order and structure to see if it can achieve what you want.