I have experienced this identical issue and am trying to work through it with a number of presets. I have never experienced anything like this in any previous firmware versions.
After doing some trouble shooting on my end, the only thing that worked for me was to open HX Edit to the problem patch, then also open the "Command Center". I then would click on the button I was programing in Command Center, in my case it was button number 3, and I was programming it to select Snapshot #5 to that button in the "HX Snapshot" control menu of the command center.
I would then select each snapshot using the dropdown menu/list at the top of HX Edit and I would see the snapshot assignment for that button change/revert back to "next snapshot" instead of Snapshot #5 that I initially programmed onto that button. I would then manually change it from "next snapshot" back to "Snapshot 5" that I wanted on that button, then I would save the patch. I would then select the next snapshot from the dropdown list at the top of HX Edit and continue to do that same process for each snapshot. Once I did this the changes were saved on all the snapshots and the patch would work correctly.
This is definitely a bug, or if not a bug, a severe unintended consequence to the new ability to stack snapshots on one button.
I have some work ahead of me to change a number of patches to get them to work correctly.
