A few months ago I posted about a mysterious bump shift that appeared after changing the transmission fluid and filter on 2003 Neon 2.0L 4 cylinder with 40TE automatic transaxle. Vehicle had about 207,000 miles on it at the time. Here is that post for reference.
I had difficulty getting the transmission pan to seal and not leak against the transmission case. I finally thought that I had it fixed after the vehicle went about 2 weeks without showing a leak. Unfortunately in early December the transmission pan gasket started to leak again. Over this time the bump shift that occurred with the first drain and refill of the transmission fixed itself as the adaptive software in the transmission controller learned how to use less pressure on the 4 - 3 downshift. It took about 6 weeks to get better and in the last month the downshift was virtually not perceptible.
The vehicle now has 214,500 miles on the odometer. This weekend I drained the transmission fluid and resealed the transmission pan to the case. I drained about 5 quarts of fluid from the transmission. I filtered the drained fluid twice and returned it into the transmission reservoir. And guess what??? The harsh 4 - 3 downshift when slowing from 40+ mph to 25 mph has returned.
Some had indicated that the harsh downshift could occur because of changing and using fresh fluid. In this situation I have dispelled that theory since I returned the exact same fluid to the transmission. So now I have another 6 week period for the transmission to relearn the proper pressure algorithm for performing the 4 - 3 downshift. This is certainly very strange indeed.
My hunch is that after draining the fluid and then refilling to the proper level, you start the engine and it takes about 30 seconds of running before the transmission pump picks up the fluid, disperses it throughout the system, and starts to engage first gear or reverse gear correctly. The transmission controller software must be detecting this very short period of no pressure and/or some air in the internal passageways and changing shift parameters accordingly.
This issue will correct itself eventually but it is annoying.