For dorrisday23, or anyone else wondering, when you go to Settings > Fancybox for WP, there is a button called Revert to Defaults. Click that, then click Save.
I am on v 3.0.6 of Fancybox. I am not sure if it is there on earlier versions.
Clicking 'Revert To Defaults' removed any malicious code on my side and I did not have to do anything within the database.
Damien