Ok at this point it's pretty ridiculous, I'm going to really need some help here.
Basically, I did the test on another computer (OSX, macbook pro). Same version of aperture and LR. Same result. So this isn't my doing I don't think. Unless I'm consistently doing the wrong mistake on both computers. Also, I've made sure that every single print dialog setting is the same. There really isn't any difference.
The other interesting thing I've found is that the only wrong color it prints is sky blue. Every single other color is fine. What the hell?!
Note the photo below, notice that the sky blue is completely off. But the blue in the water on the lower left corner is completely fine. What's going on??
You say that you tested on a different computer. Is the operating system (OSX) the same version ? Is the printer driver the same iteration ? Are the versions of Aperture, Photoshop, and Lightroom the same ?
Andrew may be correct, it may be the profile or the rendering intent. My experience is that the Relative Intent can make prints look a bit darker. It may also be a working space issue. I have read that the effects you note are exhibited when converting from a ProPhoto RGB working space to sRGB (Adobe Photoshop for Photographers, Martin Evening – page 588). However, I cannot see how this would be created by Lightroom since I understand it is effectively working space agnostic (unlike Photoshop). Jeff Schewe may want to jump in here as he knows more about this than I (but I hope this isn't another unwanted effect from the Apple colour management printing pipeline fiasco).
