Probably both instances of LAV are saving their settings to the same place. I'm afraid that not much can be done on AltDVB side - rather LAV issue (or done on purpose by LAV Filters author).
You can try to do some workaround by setting the same settings in both places, maybe that will help?
Eventual issues on LAV Filters side can be reported here: https://forum.doom9.org/showthread.php?t=156191
Report here any bugs you found