This happened to our guild prior to the patch being deployed as well. The problem seems to occur whenever you update any of the application settings. All applications, old and new get dumped back into the thread tag designated even if you've moved an application to another thread.
I haven't yet changed any of the application settings on our site because I'm dreading having to go through six pages of applications and putting all the old ones back where they belong.
We have two threads:
Applications - for those that are currently open and being decided on.
Old Applications - archived applications, accepted or rejected.
I imagine that many other guilds do the same thing. I see at least three do.
What I'm hoping for that would resolve this, is that the "Thread Tag to use for Applications:" is only applied to brand new applications, and not any of the old ones.
Edit:
I'm not sure if this is a bug as much as it is a feature change request, but I voted based on how much I'd like to see this change.