A few months ago rocksmith stopped recognizing ALL of my CDLC.  I reinstalled 2x. had steam verify integrity of files 2x. re-downloaded the D3X9_42.DLL file. nothing worked. I made the accidental discovery that  the game only sees them if I start from the rocksmith.exe file  located INSIDE the rocksmith folder. starting from steam library or a desktop shortcut does not work. If anyone knows why I am curious.  I hope this helps somebody out there. 

you probably have multiple exe files saved on your computer from reinstalling and saving or backing up the game