In addition to all my other super-secret moderator tools, (ie, knowing when you're sleeping, knowing when you're awake, knowing when you're bad or good, seeing you when you're showering, etc) I have the ability to see the number of posts that a particular user has that have been flagged.
This shows up in people's profiles next to the "mod" button, here's mine:
If I click through, I can see the posts of mine that have been flagged, and I count a total of 3. I am bad at math, but I think 3 is significantly less than 46.
I know recently flag counts were adjusted to include comment flags, but as a moderator I think I'd notice if I was flagged for comments 43 times or so.
I checked a few other users and noticed similar discrepencies. For instance, badp is bad to the bone and has 90+ in his count, although the list shows 9 (and it's paginated, although the second page is blank)