Hmm, I checked over all the comments here and didn’t see any similar reports:
https://bbpress.org/plugins/topic/unread-posts/
Have there been any changes at all to your theme or plugins recently? Also: if you use kakumei and deactivate your plugins… is the bug still popping up?
johnhiler: No changes to my theme. I did add one plugin a couple weeks ago (chrishajer’s plugin in this thread):
https://bbpress.org/forums/topic/open-target-in-a-new-window
I haven’t switched to Kakumei, and so far it’s working again. I’ll keep an eye on things…
Update: It does seem to be my theme. When I switch to Kakumei, I don’t have the problem.
I’m using a modified version of Misty for bbPress. I’ve been using pretty much the “stock” theme, aside from some CSS tweaks. Yesterday, I removed the javascript in header.php but it didn’t change anything (I thought it might be causing a conflict somewhere).
http://mundoarroba.wordpress.com/2007/05/24/theme-misty-para-bbpress/
Hey CitizenKeith… do you have a diff program like Beyond Compare?
http://www.scootersoftware.com/download.php
You can compare Kakumei to your current theme, to isolate exactly what’s changed… then update your theme with whatever changes look “suspicious”. 
It’s saved me on more than one occasion!
That’s going to save me a lot of time! Thanks John!!!
Alrighty, here’s an update: I used Beyond Compare to correct/update my theme. Everything looks good compared to Kakumei.
Right now there’s a thread on my forum that is experiencing this problem again. It’s topic ID #318 but Unread Posts is linking to topic ID #288. I switched to Kakumei and the problem is STILL there.
The problem must be with the plugin… I don’t see what else could cause this, but I’m no expert. If anybody wants to help me troubleshoot the problem, let me know. I can give you a link to my private forum via email.
We have had the same mislinking issue on our forum at: http://www.yksivaihde.net/site/foorumi/
It’s running on 0.9.0.3 because bbPress update didn’t work with the custom theme.
This plug-in also caused A LOT of queries to database and our server locked our forum out for too heavy CPU usage. I haven’t found a better plug-in for this use, but now I had to disable this one.