You need to re-set up the guitar (raising the action and examining the neck bow regulated by the trus rod) to fix the problem.
It doesn't sound like you need to adjust the intonation but re-check it after raising the bridge just to be sure.
My instructors page and www.studiotrax.net for all things recording.
my toons Brought to you by Dr BadGAS
my toons Brought to you by Dr BadGAS