I'm setting up shortcut keys for actions on a new Mac Pro (the garbage can model). When I close photoshop then reopen it, the shortcuts are gone. The action is still there but the shortcut associated with it is gone.
It's really that simple. Create action. In the actions menu, select the action and "action options". Create shortcut. Run action with shortcut. Close Photoshop. Reopen. It's gone.
Have you tried repairing permissions?
Have you saved your Actions as atn-files? If you reliad those do they store the shortcuts?
This seems to have fixed itself. No apparent reason why. After a number of reboots it just started working correctly.