Marco Arment’s (and my) “Entire Message” search in Mail.app hasn’t worked for a long time, always just inexplicably returning zero results for any search. Today it was finally causing enough of an inconvenience that he searched for a fix.
He learned that for “Entire Message” searches, Mail just uses Spotlight on the message files. So if you leave this box unchecked* in Spotlight’s preferences, “Entire Message” searches simply won’t work, and neither Mail nor Spotlight felt it necessary to tell him this. (You also need to ensure that ~/Library/Mail isn’t excluded from settings in that Privacy tab.)
He was impatient, so after fixing that setting, he told Spotlight to manually import the messages immediately:
As soon as that completed, “Entire Message” searches started working.