I have my 12 String Acoustic guitar tuned to open C (CGCGCE) tuning so that I can play Ocean - John Butler Trio, but I'm having a problem with the intonation...

If I play the bottom pair of strings open (the C tuned ones), they sound fine. Now if I fret them at the 12th fret, they still sound fine.

Now, if I put the capo on at fret 4, and fret the bottom string(s) at fret 12 again, they sound out of tune. I'm guessing this is something to do with the intonation of the guitar?

Can anyone shed some light on this matter and/or suggest how to fix it?

Thanks a lot.
Not necessarily the intonation, but it could be the capo itself. What kind is it and does it have a strong spring to provide the clamping action? Some brands of capo's will drive the notes sharp at whatever fret they are placed on, thus causing all subsequent notes to be sharp as well. You can compensate by tuning flat so that when the capo is on, all strings produce the true note for that fret.
FYI, I use the G7th and it's fantastic. It will only clamp down on the strings as hard as the player chooses, since it's the player providing the pressure on it to secure it in place. There is no spring other than a weak release spring which helps to open the capo to remove it from the neck.