I have an 09 1500 Sport. Over the past couple of years I've had an ongoing tranny problem where it clunks in & out of 4th, quite violently at times. Specifically if i'm driving up an incline and give it more gas it down shifts smooth into 2nd then when I let of the gas it slams straight into 4th. This also has been happening when down shifting from 5th into 4th.
A while back it finally stuck in 4th permanently so the dealer repaired it and said it was a solenoid issue. They replaced the unit and it worked fine for a few weeks then went back to clunking in & out of 4th gear again for the past year or so.
The dealer did a firmware update and said it might help with shift points but it didn't so I continued to drive it until it inevitably stuck in 4th gear again a couple of weeks ago.
This time they pulled the tranny and completely rebuilt it with new clutch packs.

Finally got it back after 10 days and after driving for a day it has clunked into 4th maybe a half dozen times.
Then something hit me... At no time in the past couple of years (of constantly checking with the manual shift what gear I am in to monitor the clunks) have I ever seen or felt the tranny in 3rd gear unless I manually shift it there. It shifts up from 2nd to 4th and shifts down from 4th to 2nd when gassed or from 4th to 1st when coming to a stop.

WTF happened to 3rd gear???

 

maybe it's the Transmission Control Module and not the transmission itself. Here is a quote from the 2009 service manual.

DESCRIPTION

The 45RFE/545RFE automatic transmissions is a sophisticated, multi-range, electronically controlled transmission which combines optimized gear ratios for responsive performance, state of the art efficiency features and low NVH. Other features include driver adaptive shifting and three planetary gear sets to provide wide ratio capability with precise ratio steps for optimum driveability. The three planetary gear sets also make available a unique alternate second gear ratio. The primary 2nd gear ratio fits between 1st and 3rd gears for normal through-gear accelerations. The alternate second gear ratio (2prime) allows smoother 4-2 kickdowns at high speeds to provide 2nd gear passing performance over a wider highway cruising range.
The hydraulic portion of the transmission consists of the transmission fluid, fluid passages, hydraulic valves, and various line pressure control components.
The primary mechanical components of the transmission consist of the following:

• Three multiple disc input clutches
• Three multiple disc holding clutches
• Five hydraulic accumulators
• Three planetary gear sets
• Dual Stage Hydraulic oil pump
• Valve body
• Solenoid pack

The Transmission Control Module (TCM) is the “heart” or “brain” of the electronic control system and relies on information from various direct and indirect inputs (sensors, switches, etc.) to determine driver demand and vehicle operating conditions. Depending on the vehicle configuration, the TCM may be a standalone module or it may be housed along with the Powertrain Control Module (PCM) in a single module. With this information, the TCM can calculate and perform timely and quality shifts through various output or control devices (solenoid pack, transmission control relay, etc.).

 

If you have a scanner hooked up to the vehicle go on a road test, you should be able to see the transmission shifting thru all the gears. As well as lock up and partial lock up. Did the valve body get overhauled? because there is a star case to replace the manual shift valve on the valve body, you would replace the manual shift from the 545RFE and install a 68RFE manual shift valve.