There are some known issues with 3.3.1 and live spell checking, and one of the symptoms we’re aware of is that the spell checking additions are not always showing up in the contextual menu.
Something to try is to see if the Edit ▸ Spelling and Grammar ▸ Show Spelling and Grammar menu command, which brings up a more traditional dialogue box, works better. If that does work, you may find it preferable to use that approach rather than live spell checking, until this can be sorted out.
As always, it is also worth checking against TextEdit, which uses the same text engine and spell checking as Scrivener. From what we have gathered though, this is one of those rare cases where Scrivener does work differently from the native system without any of the many additions we add on top of it.