Just to reinforce what VOS said, "Original Format" does just what the name says, and works exactly as it should.
1) set the DVR output to Pillar Box, not Original Format. The "original format" setting does not do what the name implies, it outputs the viseo based on the screen format selected in the setup.
This statement is not correct. When set to pillarbox, the HR2x is modifying the original format of an SD program by appending 40 pixels worth of pillar to each side of the frame. Setting to pillarbox may accomplish what the user wants, but it is NOT the original format sent by the broadcaster. It is a 640x480 frame transformed into a 720x480 frame by the HR2x.
Additionally, your statement that the HR2x "outputs the video based on the screen format selected in setup" is also false.
What "Original Format" does is send either a 4:3 or 16:9 aspect ratio flag via HDMI based on the format of the tuned channel. It does not affect the video in any way. Some HDTV's see and use this flag, others (Samsung included) do not. This format option was added because some HDTV's and scalers were unable to use their advanced formatting and scaling options on a signal that had a 16:9 flag. Before "Original Format" was added, the aspect ratio flag was based on whether or not the user selected 4:3 or 16:9 on the TV ratio tab under HDTV in the system setup menu.
2) I don't think 'Just Scan' on the TV is the setting you want. Typically a Justification setting will expand the programming to fit the screen. You want a setting that displays the natvie signal, usually something like "full".
On a Samsung, "Just Scan" will display whatever signal it receives across the full 16:9 frame with out any overscan (or with very little overscan if the Samsung is a RP HDTV). For an HD program, this accomplishes exactly what the OP wants. 1:1 pixel mapping for a 1080i program.
The 16:9 option on a Sammy will show a 16:9 input with about 5-7% overscan. If 16:9 (or Just Scan) is selected when the incoming signal is 4:3, it will be stretched.
If the 4:3 option on the Samsung is selected, it will append TV generated pillars to whatever signal is incoming.
Personal opinion, the HR2x pillarbox mode is very poor. I think the best way to watch 4:3 programming is to let the HDTV generate the pillarbars. The HR2x's pillar mode does not include any overscan. This results in a lot of "junk" in the gutters of the 4:3 frame being visible. Most HDTV generated bars include ~5% of overscan which hides this "junk". Additionally, the bars generated by my TV are much blacker that the HR2x bars, and much less distracting in a dark room.
The tradeoff is, of course, that when your TV is generating the bars, the guide/list is also going to be displayed between the TV generated pillar bars. For me, this is a non-issue that is well worth the improved viewing environment provided by my HDTV's 4:3 mode.