Is your SAMBC User/Data Folder somehow located inside / linked with some kind of cloud storage solution like Google Drive, MS OneDrive, Dropbox, Amazon Drive etc.?
Considering you have a server CPU in your machine, having a "roaming profile" in an Active Directory Domain would be considered cloud storage for this purpose as well.
I can't think of any reason why SAM would go back to defaults unless it can't access/read the config file inside your user profile folder.
The rotation rules are definitely stored inside the config file as you already found out yourself, so the database can not be the source of the problem this time (although it's usually our first guess for all problems with SAM
As a last resort, you might want to consider a harddrive/ssd defect => Run a S.M.A.R.T. Diagnostics tool on the harddrive where your user profile is located to verify that.