Same here. I am convinced it is mainly due to EPG data.
True Blood FXHD doubled up and with us also trying to watch a recording at the same time- the box locked up and wouldn't respond to the remote.
So I just left it and all was fine in the morning. The two recordings of True Blood were different lengths!
We had it do something similar the other night (can't recall exactly what shows/channels) where we had two recordings planned, each on HD channels and both doubled up, and all four recordings failed! (I think the box crashed and rebooted)
You have to be careful deleting the failed recordings of the doubled up shows. If there is one good recording and one failed one of the same thing, deleting the failed one can cause the good one to go too! So watch the good one before deleting both.
Last night I had a recording clash which I sorted out (Chris Ryan Ep1 & Ep2 pn Sky1 and Supernatural on Living+1 (changed it to Living to resolve the clash) and Human Target on SyFyHD) but then, with watching a recording at the same time, the box couldn't cope at the switchover time (10pm) with changing from 2 recorded shows, to 2 other recorded shows whilst simultaneously showing a recording. It locked up, crashed, and rebooted itself.
After the reboot it showed Supernatural to be OK (partial recording but got to the credits so OK). Chris Ryan had the end chopped off Ep1 and it wouldn't record Ep2 as it was series linked but had already started. (The planned recording wouldn't delete because it had already started, so I couldn't just delete the planned one and then set it going manually). Human Target behaved the same as Chris Ryan Ep2, but was able to get it on the SD channel.
The EPG issue here is where you have 2 episodes of the same show on right after each other. The EPG will often stop the first recording, thereby missing the end of the show, in order to start the second recording (sometimes you will be lucky enough to get the end of first show on the beginning of the second recording!) For instance, it did this with V on SyFy HD. Add in a 'double up' and the box doesn't know what to do first.
I think the main problem does lie with what is in the EPG data (and the extent that some channels stray from the schedule), but occasionally this 'overloads' the box (I have a SA V+), which worsens the issue. The second example illustrates this with a normal 'overload'. I think the extra load of HD especially tips the box. Bring on the new one!
(Yes, we do watch a load of old tripe on our telly, but the problem is the EPG not the content!

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Hope this helps!