When I used to transfer between two TiVo DT units, I would always have to make sure to press Live TV on the unit I was transferring from. If I were to simply start watching a show, press pause, and walk into the other room and select transfer from beginning on the other TiVo, it would behave exactly as you describe. I found that the show I was looking to transfer from the beginning (or in some cases, transfer at all) could not be paused on the screen.
Now, I have since recently changed my setup from two TiVo DT units to a single Premiere, and therefore cannot reproduce.
It may be the case being that you are transferring from a Series 2.
Worth a try, or at least something to exclude.
TiVo Premiere 4 ∙ WD 1TB DVR Expander ∙ TiVo Mini ∙ TiVo Stream
XBOX LIVE: fiftyfootfang