You are not alone. Spotlight is broken. It won't search Mail messages correctly.
So far,
nothing I've tried has given me the ability to search Mail messages under "Entire Message" for any mailboxes.
"From," "To," and "Subject" searches work, but not "Entire Message."
Doing *mdimport ~/Library/Mail* in Terminal adds current messages to an "Entire Message" search for "All Mailboxes" but does not help an individual mailbox search, nor search any new messages.
_Here's what I've tried:_
Fixed permissions with Disk Utility
Re-booted (many times)
Dragged the hard drive icon to Spotlight's Privacy window, then off again
Installed 10.5.2 from Software Update
Re-installed OS X 10.5.2 from the combo update
Ran Diskwarrior 4.1 Rev. 42, did both a rebuild of the startup HD, and Files
_In Terminal:_
Turned off indexing, then back on again
sudo mdutil -i off /
sudo mdutil -i on /
Turned off indexing, deleated the Spotlight index, turned indexing back on again
sudo mdutil -i off /
sudo rm -r .Spotlight-V100
sudo mdutil -i on /
Deleated the never index file (there was none)
sudo rm .metadata
neverindex
Tried to rebuild the index
sudo mdutil -E /
Added Mail to the index
mdimport ~/Library/Mail
Received an error message: mdimport[188:807]
* Failed to decode 8bit data, treating as binary
Doing mdimport ~/Library/Mail adds messages to the "Entire Message" "All Mailboxes" search, but no new messages get indexed.
_Genius at Apple Store:_
I spent two hours with a Genius at an Apple Store, he tried everything he knew, plus all of the above, plus asked another Genius for help. They were unable to fix Spotlight's search.
_Apple Discussions:_
I have asked this question on Apple Discussions. Several others are experiencing the same problem. So far no one has been able to come up with a solution. The number of people with this problem is growing:
Topic : Spotlight does not search Mail messages
http://discussions.apple.com/thread.jspa?threadID=1366101
Topic : Search "Entire Message" returns "0 Found" in mailboxes
http://discussions.apple.com/thread.jspa?threadID=1341832
Topic : Spotlight died on me
http://discussions.apple.com/thread.jspa?threadID=1226645
Topic : I can't search through my inbox!
http://discussions.apple.com/thread.jspa?threadID=1387827
Topic : Leopard's Spotlight doesn't search Mail messages
http://discussions.apple.com/thread.jspa?threadID=1219030
Topic : Mail Search
http://discussions.apple.com/thread.jspa?threadID=1347387
Topic : Mail Won't Search
http://discussions.apple.com/thread.jspa?threadID=1204827
Topic : Search does not work
http://discussions.apple.com/thread.jspa?threadID=1254966
Topic : Mail search not working
http://discussions.apple.com/thread.jspa?threadID=1289253
Topic : Unable to Search Mailbox
http://discussions.apple.com/thread.jspa?threadID=1232504
Topic : Why is Search in Mail.app busted?
http://discussions.apple.com/thread.jspa?threadID=1403758
Topic : Mail Search comes up empty
http://discussions.apple.com/thread.jspa?threadID=1378473
Topic : Search "Entire Message" not working with Smart Mailboxes?
http://discussions.apple.com/thread.jspa?messageID=6548355�
Topic : Mail searches yield no results! Smart mailboxes also yield no results!
http://discussions.apple.com/thread.jspa?threadID=1395508
Topic : 10.5.2 Mail.app search still not working (Entire Message)
http://discussions.apple.com/thread.jspa?threadID=1389466
Obviously, something is broken.
*PLEASE SEND FEEDBACK TO APPLE:*
In Mail, under Mail in the Menu, use "Provide Mail Feedback" to send your feedback to Apple. This sends general information to Apple about your Mail set-up, which should help them get this resolved.
If you do not wish to send them general info from Mail, you can use this link to send feedback:
http://www.apple.com/feedback/mail.html
Terrell