Mine too, J.

I ran the Clean Audio Folder tool on the audio folder and it reported none of the files were associated w/ a Cakewalk project.

I opened the CWAF and I'm in the middle of a scan of all the projects and files. Oddly, a backup folder of the projects has been created on the same drive and the CWAF pointed out to me that it thought the backup folder was the global audio folder. I've since corrected that folder path to the original.

Ok just so you might have a better idea.
The file structure should look like this.
Drive C
_______Cakewalk Projects
________________________Audio Data
 in here you will find your cwb or cwp icons and another audio folder which will have your Wave files/ all of mine are named after the song  example - Bluegoo, Audio 1, rec 2   so it's a no brainer to see what belongs to each song. I try to name my tracks and it will show as Bluegoo, Bass, rec 3
You can also create your own folders per each song and then within that folder the Audio folder will only contain waves for that song. Thats the way I do it now. Cakewalk automatically creates an audio folder within your created folders the minute you hit record ( audio)
It will also depend on how you set up a fresh song. If you use templates make sure you do a save as the first time, this will give you the option to make a new folder, name the song, and pick the cwp or cwb options.
  So try creating an audio folder and putting the tracks in it then click your song icon.

Things got weirder.

There is audio in the audio folder contained in the project folder. If you click on it, it will play.

CWAF ignored it like it wasn't there.

It found the .cwp associated with it and correctly registers that it doesn't think there are any .wav files associated w/ the project, but it didn't even register the audio existed.

Why would that be?

Ever get this figured out Kevin? I have the same problem, project opens but no audio files load, they do exist within the cakewalk projects/audio, and yes they do play. System acted weird before this happened, could not create punch in or loop points, and when recording (punching manually) only did sound on sound, new didn't replace old as it was supposed to.