For some reason, whenever I do /fly it puts my PermissionsEx group prefix at the start of my name and it can get really annoying.
Is there any way to stop EssentialsX from hooking into PermissionsEx/Vault and letting DeluxeChat do the work?

EDIT: Screenshot: http://prntscr.com/e9c28s

Sounds like DeluxeChat or another plugin is changing your display name - I'm fairly certain Essentials doesn't normally do this.

In retrospect, you most likely have add-prefix-suffix enabled, causing this. Try disabling that option and restarting your server.