It looks like I may have spoken too soon when stating we aren't seeing this with our PVR-250.
Yesterday, Jamie's Kitchen appeared to be 9 minutes long, even though the entire show was actually recorded.
My wife was having a heck of a time trying to watch it. DVRMSToolbox was trying to autoskip the commercials and the show was jumping all over the place. Each time skip or replay was pressed, it would jump many minutes in each direction.
She ended up giving up and deleted the show (mainly because I have DVRMSToolbox configured to ignore keypresses to work around a remote slowdown bug in Vista so she couldn't turn autoskip off).
STB w/R5000HD USB I/O, Gigabyte GA-P35-DS4, Quad Q6600, 4.0 GB RAM, ATI HD 3870 512MB, Ultra XVS 600W PSU, 3x SATA 500GB, 2x SATA 300GB, LG GGC-H20L, PVR-250, Toshiba 51H83 (51" HDTV), Yamaha RX-V2400 Amp, 5x Energy Speakers, SVS Sub, Harmony 880 Remote