@StuartT @kurtmacexpert It happened to me too the other day after I installed an application called File Spy (downloaded from the App Store). Just lucky to remember that.
Instead of thumbnails I only saw folder icons in my project window and the Finder did not know about the .rw6 too.
Of course I tried Rebuilding LaunchServices as that had worked before and I also had advised to do in this topic, but no dice. Darn!
Then I tried to narrow down the problem by using an old PrefPane called RCDefaultApp and found out that obviously File Spy does not know about RapidWeaver and his extensions and kind of ‘hijacked’ the .rw6 extension. RW still did open my projects, but the Finder saw them as folders.
The last update of the Preference Pane was in 2009, but it still works.
After choosing Extensions, this is what I saw:
After choosing RW all was fine 
Only the .rw6 extension was hijacked. The others all pointed to RapidWeaver.
There might be other Apps or PrefPanes to change the Extension ‘Owner’, but this worked for me and I hope for you and the others with the same problem too.
As @Turtle suggested you could create a new user account and that could fix it too, but if my solution works, it will save a lot of work.
Menno.
P.S. My version of RCDefaultApp is an unsupported Dutch localised version.