Wierd Intonation Problem

Plus, I'm pretty sure the RR1 is a recessed Floyd. Trying to move the bridge back will be a major pain.

Try some heavy gauge strings. (10-52 is too light.) Make sure the neck relief is set correctly and that the frets are properly crowned (not worn flat). These can affect intonation as well.
 
Ya, First I'm going to try with a bigger string gauge, and see what happens.

What is the process of checking the relief on your neck?

Press down at the 1st fret and 14th and check to see the distance from the 7th fret to the string. The "rule of thumb" is that you should be able to slide a business card under the string.
 
Ya, First I'm going to try with a bigger string gauge, and see what happens.

What is the process of checking the relief on your neck?

Personally, i prefer to use a straightedge and just stand it on top of the frets.
The reason for this is that the pressing down the string technique is inaccurate, as it reacts differently to different types of strings and how hard you press the frets.. but its really small differences, so its up to how perfect you want the setup.
Kind of like in this picture, but without the clock-measure:

modclapme-relief.jpg


How it should be set depends on the quality of the fret job, but as Matt says: It should be enough to slide a business card in between the string and the fret.
IF the fret job is really good, you can straighten it even more.
(More straight = more even intervals between the frets.)