If they're still missing their after rebuilding the LS database and you get expected output from "… lsregister -dump | grep 'Perform Action'" above I can give you something else to try.
I rebuilt the LS database with Onyx, verified that all files were there with grep, and Automator is still having the same problem.
Also, after I rebooted and relaunched LB, it gave me an error msg that there was "a problem" with the Applications indexing rule and it had been disabled. I turned the rule back on, restarted LB and did not get another error.
I guess I'm ready for the something else!