I had a similar problem with my kdl-46s4100. In my case it turned to be the backlight inverter board - which I figured out by disconnecting the cables to the BL Inverter board and then powering up the TV. With the BL Inverter board cables disconnected the green power light stayed on and I no longer got the 2 flashes from the standby lamp. I posted more details on another thread specific to KDL-46s4100
I also had to remove the cover from the bottom first in order to get the top to release. However, to remove the cover from the bottom I first had to file the plastic a little bit around the cable TV input jack (since it was getting stuck on this jack/connector).
I had the same problem - TV turns off and standby light flashes 2 times. I'm sure there are dozens of possible causes but I figured out that in my case it was the Backlight Inverter Board. The way I diagnosed it to this board (after I checked power supply board for bad capacitors) was to disconnect the high voltage connector from the power supply to the inverter board. I then plugged in the TV and turned it on and noticed that the power now stayed on (didn't get 2 flashes anymore). The inverter board is located on the far left side (as viewed from ..
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