One thing I've noticed that *may* have changed in the last firmware is that the way the TV handles interlaced signals seems to have changed.
I watch 1080i broadcast TV from a Virgin Media Tivo box in the UK. The TV's been running Film mode Auto 2 pretty much since I got it and it's always been fine, the TV does a much better job of deinterlacing than if I set the Tivo to output 1080p.
Watching a recorded episode of His Dark Materials last night though and there was periodic judder/frame skip which I've not seen before - setting Film Mode to Off resolved this. I think the picture quality is slightly worse with Film Mode off (seems to have less clarity and be slightly softer) but this may be placebo, not sure.
I've previously watched lots of different shows with Auto 2 and it's always been fine, so I don't know if this is something that's changed with recent updates or if it's something specific to how this particular show has been recorded. Or even a Tivo update that's caused it. This is a UK 50Hz signal and I know the TV doesn't cope too well with 50Hz (for instance Auto Motion Plus of any kind always causes skips and judder with 50Hz, so I have it disabled for this input) so maybe that's got something to do with it too.
However I'm a bit unclear as to what Film Mode is or does, and why it only applies to interlaced signals, so I'm guessing a bit here; at least disabling it seems to resolve the problem. I believe it's something to do with 3:2 pulldown so maybe it shouldn't be used for 50Hz signals at all.