New mail is not being marked as unread

This just started today. I have my preferences set so that unread mail is in Bold type. I see by the Mail Activity Viewer that new mail is coming in. Mail chimes that I have new email, but SOME of the new email is not in bold type. I say SOME because it is only a few of the messages that have this problem. I have repaired permissions, changed the mail prefs and then changed them back. Does anyone have any idea as to what is going on and how to fix it?
Thanks in advance.
PS: I first tried searching the forum, but couldn't find an answer or even a similar problem.

Thanks for the response David.
It is a POP account, actually several accounts. I am going to monitor it to see if it affects all accounts, or just one.
I am currently accessing it from my regular Mac, the G5, I only use webmail or the iBook when I am traveling.
This afternoon I ran MacJanitor and have not yet seen the problem occur, but there hasn't been too many emails coming in.
I update this thread if I find a solution and if running the CRON tasks apparently fixed it.

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