[spiderplant]

As far as I know, that fault where the timers went wrong has never happened on the V6. It was on the older TiVos, and was fixed by a software update some time ago. It was easy to spot the fault as the clock on the miniguide also showed the wrong time. I'm also pretty sure you don't have that fault because you say "Some of my recordings". If the clock was wrong, every recording would be affected.

Each case like this needs investigating on its own merits. Some questions:
1) What duration does the guide say the programme was?
2) How much start and end padding do you have set on these series links?
3) When you play the recordings, do they start at the start of the programme (allowing for the start padding), or early, or late?
4) In My Shows, how long does it say the recording are?
5) How long do they actually play for?
6) Are there any entries in Recording Hiccups that explain why these recordings were truncated?
7) Are they all exactly 13 minutes too short?

Your comment "there wouldn't be enough tuners to do it during peak times" makes me wonder if you actually had run out of tuners. Are you certain you aren't trying to record seven things at any one time, allowing for padding?