Mail marking messages after rebuild?

I was going through the process of rebuilding a mailbox stored on my Mac. After the mailbox was rebuilt, I noticed that a few messages (3 of 32) had been marked with the color brown. This is not like the junk mail marking where the text is brown; the entire message entry is highlighted much like the default "News from Apple" rule, except brown not blue. Any ideas on why this may be? The only method I've found to "unmark" is to tell Mail that the message is junk mail, then not junk mail. It seems to remove the brown highlighting after that. Any insight? Thanks in advance!
PBG4 - 15"; 1.25GHz   Mac OS X (10.4.3)   1GB RAM; 80GB HD; DVR-RW; BT; AX

As an update, I found by opening the message's .emlx file in TextEdit, there is a <color> tag in it. After deleting the color tag, the message was ok. However, this was added after the fact. Any ideas?

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