I've never seen this behavior with SV 8000 HD. It updates files slowly but surely on the memory chip. To eliminate suspicion of possible intermittent problem with hardware like Memory Controller, just load the latest bin you can find, and try again. If the problem goes away, keep this release for watching clear FTA channels.
I've seen another issue: the STB hangs at times and then reboots after adding a new channel PIDs manually and exiting from Add Channel popup menu, but this is firmware bug for sure. But some similarity exists with your issue. SW also writes to memory at dish and motor setup, and after rescanning a sat, so if you didn't have any issues doing that (unless you didn't do it often enough for the problem to show up), it looks like a firmware bug too.
Nice potato though.