I'm not sure what the issue could be, except that perhaps the FIOS remote doesn't have the correct discrete codes to power off the unit. I'm not sure there's a way to fix this, as those codes are programmed in by them.
Have you tried the other Samsung codes for that remote?
I have a Samsung 460PX hooked up to FIOS HD. I can program my remote so that it turns on the TV. But none of the codes turn off the TV. I believe it has to do with the TV remote having different ON and OFF buttons where the FIOS remote only has a POWER button. Any thoughts?