Quote Originally Posted by Ilmoran View Post
Something else that would be handy is if emotes and custom emotes were separated in the chat window filters, that way individuals could disable custom emotes from their own user experience (just like other chat methods), without removing the functionality from everyone and still being able to see the built-in emotes.
They already are separated. Just click on the little cogwheel next to the chat tabs to go to log settings, and check off custom emotes.

This completely fixes OP's problem.