It has been alleged that Dish did this intentionally because they were annoyed by people calling the support lines looking for missing channels, and it was just due to being on the wrong list.
This 'solution' however does more to annoy the users then it solves problems. (I would posit that anyone who knows enough to go in and configure a custom list, is PROBABLY smart enough to check the list before complaining about missing channels to Dish...)
Perhaps we should start calling the tech support lines and asking them to troubleshoot why our custom channel lists won't stick. If they get enough calls about it maybe they will be 'annoyed' into restoring our ability to save list settings.
I had a 522 for years and the lists always stayed where I left them. I had a 922 for about 2 years and it would randomly leave the list settings alone and randomly reset it (I think the intention is to always reset it, but like everything else in the 922, that function is too buggy to work reliably). The Hopper seems to be pretty consistent about resetting it on every reboot.