It looks like gkbisd is used for verification of code signatures for GateKeeper (the thing that asks you if you really want to open an app when you open it for the first time). It was only added in 10.9.4.
I was getting the same log messages, and found that removing its database and restarting the process stopped the messages from occurring.
Open Terminal and do the following:
sudo killall gkbisd
sudo mv /private/var/db/gkbis.db /private/var/db/gkbis.db.backup
sudo /usr/libexec/gkbisd &
You'll be asked to enter your password to run these commands.
This will kill the gkbisd process, move the database (so it has to build it again), and then restart it.
If you're comfortable with the command line then there should be no harm in deleting the database rather than moving it.