For those who have had a similar problem, there is hope as I reported in the DVR thread on the 797 software for HR44:
I got 797 [the latest software version] on my HR44 yesterday morning. I was not home until relatively late in the evening and saw that my "DVR has been updated." I have been having a problem recording games on NHL CI where if I try to start watching after the game has begun, the recording will start with an error message that "all or part of this program did not record. Scanning for recorded content." It would then jump not to the beginning of the broadcast but to the end. So, last night I set it to record a hockey game at 10 pm on NHL CI, and then started watching it 20 minutes after the recording started. Luckily, the new software seems to have solved this problem. I still got the message that the program did not record, but instead of jumping to the end, it started at the beginning. I hope this is indeed a fix and continues with other recordings.
If others are having this problem, you might see what happens when you are able to get the new software.