Hi there,
I'm not aware of this problem as I installed my own Minidisc player. Before you look at it as being too complicated, have you tried just cleaning it with a good quality CD cleaner disc? If that hasn't solved it, it sounds possible that when you fiddled with the aerial, you may have adjusted the properties of the head unit?
I'm no expert, but just trying to offer simple advice
Hope you get it fixed soon.
Jim