Finally figured it out!

HCL Notes/Domino 8.5 Forum (includes Notes Traveler)

Subject:

I'm posting this because I've just found the fix and thought someone else might be able to use this.

The spell checker was only not working for this one user. He was one of 2 people using the new template as we hadn't upgraded everyone else yet.
There is a known issue that anything within the signature box is skipped by the spell checker. So, if a user has a signature setup and they've added a few blank lines a the top of it, those lines are considered part of the signature box. So, if the user starts to type their email in those blank lines, it looks like they are part of the signature and the spell checker skips them.

It's been advised that users do not put blank lines is at this time. When a user starts a new email, if the signature is automatically appended, it leaves a blank line at the top for the user to begin their email. This line is outside of the signature box so text will get checked.

However, if the user places their cursor at the start of their signature and enters blank lines, and then types in those blank lines, they are part of the signature block and won't be checked.

Feedback response number WEBB95PMED created by ~Holly Bubponetexjip on 03/11/2013