Hi Tim,
I have the exact same problem with my Intuos Pro M and El Capitan.
I created specific settings for the Adobe Photoshop CC 2015 application, chosen by the application choser in the Wacom settings, but if I try to use them in Photoshop, always the general settings "All other applications" are used.
I recreated them, restarted Photoshop, created them with or without Photoshop running.
I am out of options! :-(