Probably just a normal LCD consequence
I suspect what you're experiencing is a "normal" effect of LCD. Remember that LCD works by blocking a back light... so if the picture changes quickly from light to dark, the TV needs to compensate by lowering the intensity of the back light. Different TV's no doubt tackle this differently... but its an unavoidable necessity of the technology. My Sharp 37" does something similar, but I hardly ever notice it... are you sure you're not noticing it more because its new and you're watching for everything like a "hawk". :-)
To try to reduce the amount you notice the effect you can probably play with the light level in the room (my TV senses this, yours may as well) as well as the overall brightness of the display. Also, play with the settings... most Sony TV's have a display mode, with values something like "Movie", "Dynamic", "Game", etc... Try the different modes... I suspect if you're on Dynamic, it might make the effect more noticeable.
By the way, once OLED's come down in price, and you can get a TV made of them, this should no longer happen... OLED's produce light themselves... so there will be no backlight... which also explains why OLED TV's are so damn thin! (If you're into thin :-)