I have found one problem thatwe are having a problem here that permissions being inadvertently wiped out after restore.
do SharePoint backups include permissions?
How can i restore site including persmisions?
If you Back up and restore content databases, then YES, permissions for the content residing in these databases will be stored along with them.
It's hard to tell what caused your problem, maybe you restored an earlier backup that had different permissions or there is something else like a workflow or event-receiver that kicked in and changed those.
When you did the backup, did you use the -includeusersecurity option?