Very Strange; Not Common
As others have already pointed out, ALL output from the TiVo, even currently playing programs, has already been recorded to the hard drive and is being played back and sent to the output jacks the same way.
I do not have a clue why you are seeing the problem you report, but I did want to assure you that it is not a typical problem with the TiVo. I use both an S3 and a THD, and I record a LOT of movies from them - most with standalone DVD recorders. I have used probably 6 or 7 different recorders (all different brands) over the years, and I have burned well over 9,000 DVDs from TiVo recorded programs, and I have never experienced the problem you describe.
TiVo Bolt 849 - 1TB - 156 HD/1065 SD, OTA
TiVo HD 652 - 2TB internal - 318 HD/2777 SD
Series 3 648 - 1TB+1TB Apricorn DVR Xpander - 265 HD/2512 SD
Series 2 - threw it away 'cause PQ sucks after HD!