I agree that the problem appears to be something strange.
As a test, 2 R5000HD users recorded Dangerous Lives of the Altar Boys on Showtime at 9:35pm Eastern Tuesday 11/29/2004 off the 110 Bird. (If you have this a capture from this time and wish to play along). All captures were edited to start at the same place and end at the same place with HDTVtoMPEG2 (though some were off up to 3 seconds as you will see).
All were then examined using MPEG2Repair with the expanded verbose error reporting.
All programs had the exact same 333k error log. They all showed the same errors at the same place - some a little more severe than others, but the consistency is clear.
For example:
Log #1
Sequence Frame 150671(710-P) / Time 1:44:20 :
Error: Motion vector going out of range at MBA=1200(0,160)
Error: Missing 1 picture slices at MBA=1200(0,160)
FileInfo: Last errors span 1120 bytes at file offset 15176910945
Error: Motion vector going out of range at MBA=1680(0,224)
Error: Missing 1 picture slices at MBA=1680(0,224)
FileInfo: Last errors span 592 bytes at file offset 15176922511
Error: Motion vector going out of range at MBA=2640(0,352)
Error: Missing 1 picture slices at MBA=2640(0,352)
FileInfo: Last errors span 578 bytes at file offset 15176939681
Error: Motion vector going out of range at MBA=4080(0,544)
Error: Missing 1 picture slices at MBA=4080(0,544)
FileInfo: Last errors span 946 bytes at file offset 15176969337
Error: Motion vector going out of range at MBA=4561(16,608)
Error: Missing 1 picture slices at MBA=4560(0,608)
FileInfo: Last errors span 726 bytes at file offset 15176978523
Sequence Frame 150739(778-P) / Time 1:44:23 :
Error: Motion vector going out of range at MBA=7560(0,1008)
Error: Missing 1 picture slices at MBA=7560(0,1008)
FileInfo: Last errors span 222 bytes at file offset 15183850121
Sequence Frame 150755(794-P) / Time 1:44:24 :
Error: Motion vector going out of range at MBA=6840(0,912)
Error: Missing 1 picture slices at MBA=6840(0,912)
FileInfo: Last errors span 130 bytes at file offset 15185468067
Sequence Frame 150961(997-B) / Time 1:44:32 :
Info: End of sequence: 1920 x 1080, 29.97 fps (with telecine flags), 18.00 Mbps.
Info: Found 150961 frames/fields since start of sequence.
Info: 766 frames/fields found with errors.
Info: 773346 corrupted bytes in file.
End of Log
Log #2
Sequence Frame 150743(710-P) / Time 1:44:23 :
Error: Motion vector going out of range at MBA=1200(0,160)
Error: Missing 1 picture slices at MBA=1200(0,160)
FileInfo: Last errors span 1120 bytes at file offset 15182411073
Error: Motion vector going out of range at MBA=1680(0,224)
Error: Missing 1 picture slices at MBA=1680(0,224)
FileInfo: Last errors span 592 bytes at file offset 15182422639
Error: Motion vector going out of range at MBA=2640(0,352)
Error: Missing 1 picture slices at MBA=2640(0,352)
FileInfo: Last errors span 578 bytes at file offset 15182439997
Error: Motion vector going out of range at MBA=4080(0,544)
Error: Missing 1 picture slices at MBA=4080(0,544)
FileInfo: Last errors span 946 bytes at file offset 15182469465
Error: Motion vector going out of range at MBA=4561(16,608)
Error: Missing 1 picture slices at MBA=4560(0,608)
FileInfo: Last errors span 726 bytes at file offset 15182478839
Sequence Frame 150811(778-P) / Time 1:44:26 :
Error: Motion vector going out of range at MBA=7560(0,1008)
Error: Missing 1 picture slices at MBA=7560(0,1008)
FileInfo: Last errors span 222 bytes at file offset 15189350437
Sequence Frame 150827(794-P) / Time 1:44:26 :
Error: Motion vector going out of range at MBA=6840(0,912)
Error: Missing 1 picture slices at MBA=6840(0,912)
FileInfo: Last errors span 130 bytes at file offset 15190968195
Sequence Frame 151047(1011-B) / Time 1:44:35 :
Info: End of sequence: 1920 x 1080, 29.97 fps (with telecine flags), 18.00 Mbps.
Info: Found 151047 frames/fields since start of sequence.
Info: 766 frames/fields found with errors.
Info: 773346 corrupted bytes in file.
End of Log
Same number of frames/fields with errors, same number of corrupted bytes - virtually identical.
Thus, it is not a SINGLE Dish Receivers. It either has to be originating out of R5000 Dish 6000 units or out of the Dish chain
A test was set up with several 169time users and a C Band user and even someone with an open cable box not on Dish for reference over this past weekend, however.....guess what happened?
The cap of The Postman was error free for the 3 hours it was on. Same with the first 8pm Saturday showing of The Last Samurai.
As no R5000HD software was changed, it does seem suspicious that this was the case. You would think if it were the software, it would be consistent in errors.
Now, Antone Fisher caused a file restart every showing in mid-November over the course of a week. Yet a week later, no issues.
It would seem that the same input should cause the R5000 to behave the same way every time. Yet it seems that the problem exists and other times it doesnt.
BTW, as a side note, as Dish allows you to view the same PPV all day for the same $5.95 price, Passion of The Christ was capped every showing for a day.The bit rate was significantly better for the first 2 showings (at 10am and 1pm) than later on in the day/evening (starting with a 5pm showing). Thus Dish does play around with these things.
This, quite simply, is why an apples to apples comparison will only work off the same capture at the same time, though the post about this being a 110 satellite issue is interesting.
Again, the final and conclusive test will be off Dish via 169time and R5000HD when the problem occurs again - most likely during the next week.
But it is looking less and less as its the new R5000HD software causing all the errors in the captures.
As for the R5000 not starting - always deciding to do this on 1 time showings or limited scheduled items, usually waiting for drive or other error messages thats a different issue.

And finally, does anyone know how to add recording time to a capture in progress? You can do this with MyHD, but when you hit OTR on the R5000HD to more time, it stops the current recording and restarts it - thus ruining your cap.
Thus, if HDNET only shows The Wall once every 6 months and it starts 30 minutes late as it did Sunday Night, you are hosed trying to add more time to the capture.