Welcome to the world of Color MIS Management
I've got mine close so I'll try to explain my set up.
I let my application control color so I've turned off Color Correction on my Pro 9000.
Go To
Pro 9000 Properties
On Color Intensity click 'SET'
On Matching Tab click 'Color Correction', set it to 'OFF'
This will allow your application to control the color.
Your Monitor Profile should be set to whatever you named the profile from Color Munki. Your Color Munki Profile should also load into the LUT at start up.This is a Windows term but all it does is load the profile into the Video card.
Your Printer Profile should be set to your Color Munki Profile you created for your paper. This profile is good for only the paper you created it for.
Using these settings I get my prints very close, the difference being a back lit screen vs. Photo Paper.
I read at the Qimage Forum about a color problem regarding OS 10. You might go there and see if it applies to your system. They have a work around.
I run RGB color space also and have no problems.
Here's an interesting link that helped me when I first got my Pro 9000:
Canon Pro 9000
Good luck.