Has anyone else had problems getting the message filter to work?

I'm using ISE 11.3, I have "enable message filtering", "display incremental messages", and "enable enhanced design summary" selected in the design properties as well as in the design summary panels. Under "All Current Messages" in the design summary, I have the Warnings box checked under Show Messages.

I think I've been having this problem since 11.1. I used to be able to fix it by ensuring these boxes were checked. I recently moved to 11.3 and now I have a design where it doesn't work no matter what I do.

I use "copy project" a lot, and I wonder if that has anything to do with it.

Also, when I right-click a warning in the project navigator warnings window, it does not give me the option of filtering the messages from there.