I am experiencing this too after the update, I have to type in full
application names to get the "Run" option, and then there is no icon.
Here is my terminal output, but I couldn't find the log file at the
location you describe, Chris.

** Attachment added: "gnome-do-output"
   http://launchpadlibrarian.net/18347607/gnome-do-output

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GNOME Do 0.6.1.0 fails to index launchers (.desktop files)
https://bugs.launchpad.net/bugs/280365
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