My keyboard shortcut System Preference panel doesn't allow me to create application shortcuts My computer is a MAcbook pro and I am running Macosx 10.8.4
I just realized that the shortcuts don't work anymore in an application where I really need them. When I went to re-create them in the keyboard System Preference panel, I wasn't able to do it. I could select my application, and name the shortcut I wanted to create, but then it was impossible to type the actual shortcut. I got error beeps and no symbol would appear. 

I don't know what to do at this point.

Are there some commands I could run in Terminal to fix this issue?

Thank you
After you have selected the shortcut you want to change, press the tab key on your keyboard and you will be able to type in the new shortcut.

Anyway, that is how I solved the problem :-)