Just found a very old bug, found while reviewing #3709.

After the UserPreferences in Eclipse are read from the disk, they are stored in the project session property and the value is not changed even if the underlined properties file is changed on disk, only if the user changes preferences via UI.
So just opening the .settings/edu.umd.cs.findbugs.core.prefs in the text editor and changing any value doesn't make any difference on followed analysis results.

The fix is trivial, I will push a PR in a moment.