Hi!
I’ve got similar problem with lightbox gallery.
On my site: http://www.twoje-schody.pl there is small gallery (3 pictures). When someone want to to open (click) the photo the lightbox is running but only for 2 seconds and later the picture is open in browser (like as link).
I checked that the gallery got this short code: [gallery link="file"]
What can I do to fix it?