If the transmission works fine, except for the 4th – 5th shift, I would suggest that it is an ‘electrical’ problem. There is a number of sensors – solenoids – control unit – that controls how and when the transmission shifts.
The dealer should be able to tell you exactly what’s wrong with your transmission by running the diagnostics on your car.
Let us know the details.
Regardless of the response from the dealer, get a second opinion. At $3,500.- it’s worth the effort.
If all the electrical checks out fine and IT IS a ‘mechanical’ problem with the transmission, I would start experimenting with the ‘transmission fix’ products from Lucas Oil. At that point, you have nothing to loose and quit a few have had great success with this product.