I have seen this before, back when I still had a ViP722k. I was able to fix the issue by simply replacing the separator attached to the back of the receiver.
Interesting. First I had my 612's get flaky on their second tuner. Dish replaced both. Then my 722 went all squirrelly with decoding the stream, and I had that replaced as well. I never replaced the separator on any one of those receivers, and the new receivers worked fine until I "upgraded" to the H3.
The only issue I ever had with a separator was when one of my 612's got into a boot loop on "boot recovery mode". I left it in that sorry situation for days, never getting a complete firmware download, until I gave up and reversed the leads from the separator to the 2 tuners. That fixed it immediately on one boot/download. I concluded that something was wrong with the recovery bootloader in the 612 (at least at one time) which prevented it from getting new/updated firmware over the bandstacked frequency band.
You reminded me of this in another thread about your Wally.