I’ve been having a problem with mail – I can’t do a search on ‘entire message’. It is greyed out. There are all kinds of ‘fixes’ available on the internet, but most of them didn’t work. Finally I fixed it and here’s a summary of the most useful advice, try it in this order:

1. Have a look in ~/Library/Spotlight and make sure there are no plugins that might be causing problems. For example, I had an old Mailtags Plugin that was 2 years old, so I deleted it.

2. Make sure you haven’t excluded your mail folder in the spotlight privacy tab (spotlight preferences)

3. Reset the entire spotlight database by opening a terminal window and typing 

sudo mdutil -E -i on /Volumes/*

(It will ask for your password)

4. Open Mail and click on Mailboxes:Rebuild.

That resets spotlight and mailboxes, which I think just about covers all options.