You might as well uninstall the other apps, run the cleaner tool (google it) and reinstall all your Adobe apps. Probably the best bet from what you describe.
I ran the cleaner tool and restarted. In the dock now PS has a question mark and indesign is gone from the dock. It this normal and can I install the dmg file?
I have never used the cleaner tool before. (I choose the CS6 clean option when I used cleaner tool program.)
Also to mention, after the cleaner tool and restart the CS - AI, DW, FL, FW icons still show in dock but the adobe media encoder CS6 icon also shows question mark along with the the PS.
It sounds like a system problem. I would test your hard drive.
Or try running from another user.
I reinstalled dmg file of creative suite and everything works fine. Not sure if cleaner tool was helpful or not.