I've got an issue that recently came to my attention. Comments left on the two blogs I have running on my server are not appearing anywhere. At all. If a user leaves a comment, they get the standard "your comment will be moderated" screen. But the comment never appears, nor is there any mention of it on the activity log. The comments USED to work, then stopped.
The only change that I can think of is that I raised my spam threshold to a more aggressive number, because I was getting a lot. But I lowered it back, and no difference.
Any ideas?
Here's the setup
MT 4.01 on Windows Server 2003 R2 using IIS 6.0 The blogs are www.restlesslikeme.com and www.thedirtytrickscampaign.com

Interesting. Here are a couple of things I might consider checking:
there is a filter for viewing all "Comments marked as spam" in the comment listing sidebar. See if you can find your comment there.
but nothing is in your activity log? yikes.
do you have asynchronous publishing turned on?
what does your mt-config.cgi file say for CommentScript? Anything?
Wow. The comments were in the spam portion. Interesting, considering that all the comments (both spam and regular) would appear in the 'waiting to publish' section. What's a good sort level?
Still nothing on the logfile, though.