I found this in the user manual which does support your understanding of how the recording works:
Freeview+ HD explained:
• Accurate recording
The start and end times of scheduled recordings will track the signal meaning the recording will start and stop at
the times sent by the broadcasters. If a programme starts early or runs late the record time will automatically be
adjusted to record the whole programme.
But at the bottom of the page it states:
Note: The above Freeview+ HD features are available on channels where the correct and accurate data is being
broadcast. Some channels may not support all of the Freeview+ HD services.
For more information on Freeview+ HD please visit
http://www.freeview.co.uk/HD.
So it seems the channels you have problems with do not support this feature