Paxton, read some threads and let the system catch up and you should see threads only being marked unread when they actually have new posts. The new style uses the database (rather than cookies) to keep track of what you've read. Works better if you're browsing from multiple computers.
Once you guys have caught up on posts (or marked all as read like Dan suggests) and if you're still seeing the issue, let me know and I can adjust. I do find that it works quite well once you've caught up.
Alright, no problem.
Do inform us when we can start donating. You need something for your effort, if only to cover your expenses.