Hushkal found this bug: If you attach a custom avatar and then try to upload an emote, it will appear to upload fine. However, the emote doesn't appear in the emote library after upload.
If you use a default avatar and then upload the emote, it uploads fine. You can then attach the custom avatar again and the emote appears in the emote library.
Here is a clip demonstrating the bug:
Here is an fbx for an emote to reproduce it: