Logos

The US Blu-ray with the Theatrical Version contains a Warner logo at the beginning while the Extended Version contains a Sierra Affinity logo.

US Blu-ray (Theatrical Version)	Screener (Extended Version)

Alternate
01:29-01:42 / 01:22-01:35

Right after the title, an alternate take with the Christina Hendricks credits follows in either of the versions.

In the Theatrical Version, Franky is running across meadow. Then Billy lifts him up. It matches Hendrick's first appearance.
In the Extended Version, Franky is crossing the street. A car has just driven by.

Extended Version 0.1 sec longer

Theatrical Version	Extended Version

01:45 / 01:38-01:48

Additional shot of Franky Walking around.

10.1 sec

Alternate
01:51-02:03 / 01:54-02:05

In the Theatrical Version, Franky comes home and sits on a chair.
The Extended Version shows him outside.

Theatrical Version 1.7 sec longer

Theatrical Version	Extended Version

02:09 / 02:11-02:16

Extended shot of frolicking Franky.

5.4 sec

Alternate
02:15-02:28 / 02:22-02:36

Only the Theatrical Version contains a shot of Bones and Franky playing hide and seek. Then an alternate shot of Franky during the next credits. After that, another shot of Franky outside - only in the Extended Version.

Extended Version 0.3 sec longer

Theatrical Version	Extended Version

Alternate
02:37-02:56 / 02:45-03:06

In the Theatrical Version, Bones finds a note from Billy on his winshield. Billy looks out of the window contemplatively.
In the Extended Version, Franky keeps running around unburdened. Billy is looking for him a bit panicked.

Extended Version 2.2 sec longer

Theatrical Version	Extended Version

03:05-03:23 / 03:15

Additional shot of Franky and Bones in the Theatrical Version: The latter is jogging on the spot next to the car while Franky is behind the wheel. That makes it look like he was actually driving the car.

+ 18.2 sec

Alternate
03:32-04:05 / 03:24-03:51

Entirely different order of events until the second producer credit.

The Theatrical Version contains several black light shots, then Franky and Bones in the child's room.
In the Extended Version, Billy keeps looking for Franky plus interuts of the interior of ruinous buildings. Her finding him is the shot from the Theatrical Version with the credit of Christina Hendricks.

Theatrical Version 5.8 sec longer

Theatrical Version	Extended Version

04:11 / 03:57-04:02

In the Extended Version, two shots of fire are longer at the end/beginning.

4.8 sec

04:27 / 04:18-04:58

Additional scene after the last credit: two girls are chatting and Bones appears. He mooches a smoke. At the end, the girls mention Mr. Skip was moving out which introduces the following scene with Mr. Skip explaining his motivation to leave - also in the Theatrical Version.

40.8 sec