I might be able to add something to this.
I had a similar problem with spell checking sometimes working and sometimes not. Yesterday spell checking seemed to be working a project I’m working in, but today inline checking seemed to not be working.
I tried turning it off and on, changing the language to “auto” and back to English, etc. I also tried making a copy of the project.
None of these things made the problem go away, but one quirky thing happened that may be useful: On one of a few occasions, a single erroneous word was identified, the first one in the document. On other occasions, and I can repeat this again and again, if I tell scrivener to check spelling now, it finds the first, and ONLY the first misspelled word. If I move the cursor beyond that word, and pick “check spelling now” again, it finds the next misspelled word, but only that one.
Spell checking in line works for other apps.
I’m using Mountain lion, and it is updated, and I’m using the app store version of scrivener.
When I select “System text preferences” from preferences nothing happens that is supposed to happen (I think) but some errors show up in console. I’m going to try to document that here.
So, I start scrivener. Open the document. Turn on Check Spelling while typing. Type misspelled words.
The words are not underlined and console does not show any error.
Then, I move the cursor to the front of the document and select “check spelling now” and it finds only the first one. Nothing on console yet.
Then, I go to preferences, and select “system text preferences”
The control panel for the OS opens in the background not showing any particular panel, just the “all” view. And, the following errors appear on the console:
5/2/13 11:08:58.536 AM appleeventsd[48]: Sandboxed application with pid 654 attempted to lookup App:“System Preferences”/672/0x0:0x92092 sprf1000 sess=100003 but was denied due to sandboxing. (handleMessage()/appleEventsD.cp #2067) com.apple.coreservices.appleevents.peer.0x7f9f72607b00.xpcq
5/2/13 11:08:59.000 AM kernel[0]: Sandbox: sandboxd(673) deny mach-lookup com.apple.coresymbolicationd
5/2/13 11:08:59.048 AM sandboxd[673]: ([654]) Scrivener(654) deny appleevent-send com.apple.systempreferences
Hope this helps!