It looks there was an issue with an upgrade somewhere along the way.  I saw that the "exclude forums" settings were shown twice rather than once.  I fixed that and it seems to behave properly for me.  If you're still having trouble, try "Reset Exclusion", save, then go back and re-edit to set whichever forums you want to ignore.
Hopefully the problem is fixed now.  If not, let me know.  Thanks!