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pjm13,
Those numbers should not be high enough to be an issue.
The debug log should list a lot more output and have timestamps indicating when each line generated. When running in debug mode, Calibre automatically shows you the debug log txt file when you quit.
It's vaguely possible that there's a problem with one of the specific emails in question. I would try manually marking all but one read and trying it again, then marking each of the problematic emails unread one at a time and trying it to see if the problem can be narrowed down to one email.
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