My setup:
Sony Bravia KDL40CX520 TV
MagicTV 3600
Sony BDV0-E2100 home theatre
I've got the aerial coming in from the wall and going into the MagicTV's aerial in. Then another cable from the MagicTV aerial out into the TV aerial in (i.e. they're daisy chained).
There's also HDMI cables between the MagicTV to the TV, and from the home theatre to the TV.
If I'm watching the TV (straight TV, not via MagicTV box) with the home theatre off then I can get all channels. If I turn the home theatre on then I lose Prime and Choice (all other channels work) and the TV reports "No signal".
Watching TV via the MagicTV box lets me see all channels with both the home theatre on and off.
Why would the home theatre interfere with Prime?