From everything I can tell, this IS a set-up issue. If the OP has an AutoConnect mower with Independent Lift, there are still two latches that need to be closed after driving over the deck. If everything is not set-up correctly those two latches (or sometimes just one of them) cannot be closed / latched. The reason I wanted your S/N is so that I could contact the Area Service Manager on your behalf as this seems to be a DEALER issue NOT a DEERE issue. Again - I am basing that statement on what I can tell from the posts.
A - Your dealer should have asked you how you were planning on using the equipment and sold you the correct set-up - even if they had to wait to get a mechanical lift system. You have 3 main choices: 54D or 60D deck, Mechanical or Independent Lift and Manual or AutoConnect PTO. Any of these options will work with any of the others. Want 54D with AutoConnect but Mechanical Lift? Not a problem. 60D with Independent Lift and Manual? Again, no problem. I am thinking that the dealer did not ask these questions and sold the OP what they had available or what was close to coming in.
B - Incorrect installation / adjustment will cause the problems the OP is experiencing. In a case like this the Dealer should NOT charge for pick-up and delivery or at home service. If it was a regular warranty issue then pick-up/at home is not included in the warranty although many dealers include it as part of thier sales process. New paint will not cause the issues I believe he is having.