I've just noticed that the default note font setting does not work. I don't know when it stopped: I decided not to use Mori for ongoing work until various bugs were fixed. So, put differently, this issue may have appeared in version 1.6.10 for all I know.
I've set my default note font to be Helvetica 18, but any new note continues to use Lucida Grande 12 pt. This persists with quite/restarting, new notebook, etc. It may be that I'm doing something wrong, but not being able to reliably set a default note font size makes things hard on my eyes!
works here
The default font setting works for me (Mori 1.6.11/MacOS X 10.4.11/Intel). Did you try to remove Mori's preference file to see if it might have become corrupted somehow?
It's located at "~/Library/Preferences/com.apokalypsesoftware.Mori.plist"
"~" is a shortcut to your home folder.