There wasn't any trash to delete on that site. There was a single trash post in one of the other sites. I deleted it, but the behavior hasn't changed.
I checked my tables. They are all OK.
There are some private posts, but they aren't being miscounted, best I can tell. The Legacy category contains one public post and no private or deleted. The FAQ category contains 6 private posts, but none of the private ones also have the "AMBER" tag. The other two private posts are in category "HOW-TO".
There are more incorrect entries in the table now than there were when I first posted this. For example, there are actually 2 Tutorials, total, and neither has tag GLYCAM or Glycoprotein Builder. But, both have do tags "BFMP", "Downloads", "ring conformation" and "Software". Only "ring conformation" shows up as a tag for them.
I just tried changing the label (not the slug) for "ring conformation" to "Ring Conformation". I know I had done that for other tags, but doing that didn't change any behavior that I can tell.
I said this before, more or less, but here it is in clearer form:
In the table at the URL below, the tag "AMBER" has 0 FAQ entries and 1 Legacy entry. However, there are actually 3 FAQ entries (all public) and no Legacy entries.
If you use the URL to access the info, it comes up correctly, logged-in or not:
3 posts (correct):
0 posts (correct):
3 posts, total, with tag AMBER, all public and published:
Let me know if there is any other troubleshooting I can do.