First the auto sync feature only works if the corresponding TV also supports it, and most do not, it's a very misunderstood setting. I keep mine off. Second, did you change any setting on your TV in regards to motion control, like Samsung's Auto Motion Plus? If you did, the TV is taking a bit longer to process the video when you turn this setting from off, to min, to max. Seems to me that if you are experiencing sync issues with the same disc, then something had to change. If it is a streaming source, then that can be a bit of a crap shoot.
I have a Samsung D606420 LCD TV with AMP set to Clear (low), fed by an HDMI cable from my X2000, and I require a 110ms sync offset verified using both S&M2 and WOW calibrations discs. Mine is very consistent between sources like DirecTV and Blu-ray, but is still sometimes off using Amazon Instant. When I switch AMP to Standard (more aggressive) the sync needs to be at 160ms
EDIT: I should also add that TV shows on DirecTV can be a bit of a crap shoot from one channel to the next. For me, TBS is un-watchable due to how bad their sync is compared to every single other channel I watch. Also, not every show on Amazon Instant is off, it also varies from show to show, but it's always tolerable.
Samsung UN60D6420 ~ DirecTV HR-44 ~ Sony S5100 BD ~ Roku 3 ~ Denon AVR-X3200W ~ SVS Prime Bookshelf L/R ~ SVS Prime Satellite Surrounds ~ MultEQ XT Flat / DEQ OFF~ Power Sound Audio XV15