I've read these and they do not appear to pertain to my situation but I have done more testing and I think I have, at least for myself, isolated the problem so that it no longer effects me.
I discovered that when I would empty the recycle bin, all by itself, not using CCleaner, that the restore points would be deleted.
I uninstalled CCleaner and tested the Empty Recycle Bin feature and the restore points were fine.
I re-installed CCleaner leaving UNchecked any of the boxes relating to the recycle bin. Now I can run CCleaner with the Empty Recycle Bin option selected, as well as use the Recycle Bin on its own, and neither are deleting the restore points.
I tested all of these several times, while also restarting the computer, so I am fairly confident that this was the problem.