Thinking about this a bit more it makes no sense.
Say you are watching a HD channel. The Video Data data is compressed using the H264AVC codec and the audio with aac (advanced audio codec).
SD channels use mpeg2 (same as DVD) and mpeg1 layer 2 audio (MP2) audio.
The tuner extracts these streams, This stream of data is digital so when you record it it is simply copied to a hard disk file. The file is exactly the same as the original transmission. The same applies to when the current tuner stores the live stream to the time shift buffer file.
That's why true pvr's record in exactly the same quality as the original broadcast.
This isn't true for DVD recorders. The data is recoded, depending on the bitrate used the recording can be made smaller than the broadcast at the expense of quality.
The audio and video compression is removed within the box decoding module, the now much larger amount of data is transmitted over HDMI to the display device.
The same bit of the box handles the audio and video decoding process. The only difference is where the data come from. It is either the live tuner output, the time shift buffer file or the actual recording file.
How can the same data produce problems when delivered direct from the tuner rather than from a exact copy from the box HDD.
Answers on a postcard please. 
I can only think it's a issue in the direct signal path from tuner output to decoding module in.
The playback of an entire programme succesfully using chasing playback might help to confirm this hypothesis.
