Sometimes this is still a different clutch related issue. It has sometimes been resolved by bleeding the clutch or by replacing the clutch master and slave cylinders. This can happen if the clutch sometimes does not fully release.
It might also help to change the transmission fluid. Shifting quality is improved by adding friction modifier to the fluid. There is a FAQ about making the transmission "cocktail" with Mobil 1 ATF and Ford friction modifier. Non synthetic Mercon ATF with added friction modifier also helps. Some, including myself, are using the Chrysler spec ATF+3 that already has a higher level of friction modifier. New fluid with friction modifier might not solve the issue you described, but it will greatly improve overall shifting quality.
