Comment 8 for bug 998759

An indicator refresh would cause a check of the usage database if there was a search active, as it could possibly change the ordering of the search. Though, it sounds like that's not the case here.

Not sure of the exact cause, but a work around would be to tell the HUD to not save usage data so it'll only use an in-memory database:

  $ gsettings set com.canonical.indicator.appmenu.hud store-usage-data false

Which would mean that the locking files wouldn't be checked as the database is read.