select "smart quotes" context menu:

that menu should have check marks?

This doesn't seem to work for me. If I select the "Show Substitutions" menu item, the selections I make (remove check marks from Smart Links and Text Replacement) don't seem to stick after restarting FSNotes. Also, I don't see any check marks as shown in @gingerbeardman's graphic above.
EDIT:
I missed @gingerbeardman's comment that his issue had to do with the context menu, which does now show check marks. Should the top-level menu also show check marks?
Ah, I see what you mean in the FSNotes Edit menu.
It's only been corrected in the Context menu, where I see this:

Deleted--see below.
--
My discussion of this issue is a bit jumbled, so I thought I would try to clarify.
From the top-level menu, when selecting Edit > Substitutions, no check marks are shown.
From the top-level menu, when selecting Edit > Substitutions, the selections I make do not stick after a restart of FSNotes.
From the context menu, when selecting substitutions, the selections I make do not stick after a restart of FSNotes.
I tried deleting the FSNote preference files to see if that might help, but it didn't.
Thanks.
FSNotes 1.9
I installed FSNotes 2.0 and all three of the issues noted in my post above have been fixed. Thanks.
Thanks!
Most helpful comment
My discussion of this issue is a bit jumbled, so I thought I would try to clarify.
From the top-level menu, when selecting Edit > Substitutions, no check marks are shown.
From the top-level menu, when selecting Edit > Substitutions, the selections I make do not stick after a restart of FSNotes.
From the context menu, when selecting substitutions, the selections I make do not stick after a restart of FSNotes.
I tried deleting the FSNote preference files to see if that might help, but it didn't.
Thanks.
FSNotes 1.9