This is a pretty vague problem description, but frequently the problem with print not matching screen is that you don't have a calibrated monitor.
Most folks seem to have the monitor brighter than optimum.
I edit my prints in a room with no overhead lighting and use a desk lamp so that no light shines on the monitor. If I put my hand on the monitor surface the back of my hand is dark; no light shinng on it.
Go to this website: http://outbackprint.outbackphoto.com/printinginsights/pi049/essay.html
and download the test image and see how that prints without making any adjustments. The test file is properly exposed and adjusted for color, so that will tell you if your printer is functioning OK.
I would also suggest you adjust the monitor brightness and contrast to 50% level as a starting point.
The ColorMunki isn't calibrating your printer, its calibrating your monitor.
As a test, adjust your monitor brightness up and down, print an image at each setting, and you will see that all the prints will look exactly the same since you haven't affected the digital file.
Calibrating your monitor sets it to the brightness that will replicate the printer output, so when you adjust an image in your processing software to look how you want on screen you will be sure thats how it will look on paper.
Here are some excerpts from a document that Canon supplies with the Print Studio Pro software.
Since you already have the calibration tool you should definitely use it. It is 30 minutes well spent.
I have the Pro-100, and I can tell you it makes stunning prints.
A far easier way to get the two closer is, contrast, brightness and gray-scale. You can adjust these with what came with your computer and monitor. Nothing else!
If you get these settings correct most likely you will be happy. Remember you are comparing light on a screen to pigment. They are two very different properities.
All those color gagets are probably useful to geeks but not for use meer mortals, get these three right and move on to great prints.
And keep in mind you are not likely to get every single color to match no matter what.