Confirm you reopen the same edition and copy stored in Applications. App Store, direct, and beta copies can maintain separate settings.
Change one setting, quit diCleaner normally, and reopen it. If the app was forced to quit immediately after a change, make the change again and allow a few seconds before quitting.
Remember that thresholds and ignore rules affect new scans, not an already open result.
An organization profile or read-only environment can enforce settings. Contact the administrator for a managed Mac.
If the issue continues, record the exact setting, before-and-after values, edition, version, and whether all preferences or only one are affected.