Imported 40,000 emails - what does "updating color for messages mean"

I have just imported 20 MBOX files from my outlook 2011 - a fair amount of emails!!
But I'm finding that when I click onto the folders, I am getting nothing in teh preview initially sometimes and... some of the folders begins some kind of scan? progress in activity panel say: "updating color for messages"
Any idea of what is going on? I am new to Mail 4.5...
I will probably be upgrading tomorrow to lion, so perhaps it won't do this anymore after that?

ok thank you.
on another note, does rules actually work? you see I have all these Mail Boxes in Mail now. and I set up a rule so one of my guy's emails goes into their folder when hey send me an email and then when I send to them? but its just not happening? see:
Any ideas?

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