Spotlight suddenly not listing email messages

I noticed today that Spotlight wasn't listing recent emails when I performed a search of known content in a message. I could use Spotlight to find older emails just fine.
In the mail app itself, I can use search with "Entire Message" selected and it will find all messages including the very latest ones. As I understand it, Mail uses Spotlight to index mail contents.
I tried reindexing just the mail folder by adding it to the privacy pane in Spotlight settings then removing it again. I noticed that reindexing was taking place but once complete, Finder or Spotlight wouldn't show any results at all - not even for older emails.
I tried a full reindex of the entire drive with the same result. I can find emails just fine within the mail app but not using Spotlight.
If spotlight wasn't indexing the emails, I don't think I'd be able to find the emails in the mail app so there is clearly some other issue preventing Mail Messages from appearing in the standard Spotlight results. I've tried unticking Mail Messages and then ticking it again in the Spotlight preferences.
I recently installed the latest security update for Snow Leopard. I don't know if this is somehow related as I believe the Mail app was modified.
Anyone have any ideas please?

To update.
I've performed a permission repair using disk utility.
I've also copied the Envelope Index file within the Mail folder to my desktop and then relaunched Mail to let it rebuild it.
If I type in Spotlight kind:message, it is listing a single email but only one I happen to have in Library/Mail Downloads. Interestingly, the one it finds is of extension .eml whereas all of the email message in my main mail folder are .emlx files. Any relevance?
Message was edited by: Doyden

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