Mail becomes unread after rebuild

I just performed a rebuild on two large mailboxes in Mail and had a strange result: first, the reported number of messages in the box increased significantly (over 300 added), and second, a lot of messages were now set as unread. There did not seem to be any immediately obvious link: dates, size, sender etc. It looked almost random.
Any ideas why this might happen?
Should I be more worried than I already am?
Gavin

It was a first time run. Mail had become very sluggish in launching and a print article I'd read suggested this as a course of action.
There were about 1000 messages in each of the two mailboxes and about 300 more afterwards.
The total Mail folder (library/Mail) is just over 508 MB. One of the mailbox folders is 28Mb and the Inbox is 53 MB. So well under the limit, I'd say.
Gavin
PS Loved the amazingly quick response to my question, by the way!

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