This so interesting to read!
I have IDENTICAL issues as you but on totally different DVB S/S2-cards, 2 x Digital Devices Cine S2 with DuoFlex add on card to get 4 tuners per card, totally 8 tuners in my setup.
I was searching on the web for solutions on "continuity counter errors" . I use TVHeadend 3.9 on Ubuntu 12.04 LTS with Digital Devices Cine S2 dual tuner card with DuoFlex add on cards to get quad tuners per tuner card.
I also see that it is always the 2nd tuner chip that gets these problems, i.e. Tuner 1 works fine on HD channels but tuner 2 gets Continuity Counter errors when tuning in to HD channels. Tuner 3 works fine but then again tuner 4 gets CC errors... If I disable every 2nd tuner, i.e. tuner 2, 4, 6 and 8 in my setup so that my software only uses 4 of my 8 tuners it works fine.
If I remove my 2nd card AND remove the DuoFlex addon card from the remaining Cine S2 card so that I will only have 2 tuners left, I STILL get the same problem, i.e. tune into HD channel on tuner 1 works fine but as soon as I tune into a HD channel on tuner 2 I start to get artifacts/pixelation and CC errors.
See my full comments on this in the thread at
viewtopic.php?f=37&t=8278&p=31680#p31680