Why was the John/Jigsaw Autopsy in SAW IV ignored?
A lot of theories deal with this. One major one is that not only is the autopsy scene after Saw IV, but after Saw V as well. Here's the order of things that we can guess:
(1) Hoffman traps Strahm in the sick room / Strahm gets stuck in the head box trap and escapes,
(2) Hoffman is promoted / Strahm continues investigating the "accomplice".
(3) Hoffman finally gets Strahm where he wants him, and not only frames him, but kills him as well.
(4) After Strahm's "disappearance"/crushing and Hoffman's escape in the glass box, the autopsy on Jigsaw is performed.
(5) Hoffman gets the call, arrives at the morgue, plays the tape. The games have just begun. Another "clue" is that the end credits music for Saw V is "Just Begun" from Saw IV, the music that plays when Hoffman first arrives at the morgue and plays the tape at the beginning of IV.
Overall, these are just theories, as usual in the Saw series. However, even Jigsaw himself says that "all the pieces will come together."