Hi,
Fundamental problem is the baseline to use. If I go to my monitor control panel, there a re myriad of preset options for colour and brightness. Under colour, there are all the usual suspects like Adobe RGB, sRGB and Custom where you can create a seemingly infinite number of configurations.
The one to use is Custom. I have an Eizo monitor with numerous pre-sets and the instructions make it quite clear that "Custom" is the one to use when calibrating yourself. You must then keep the monitor in that mode for all colour management aware applications.
You are right to leave the Contrast & Brightness at "native" settings, but if you use the advanced mode of the calibration software, you will probably get the option of setting the brightness to obtain a target luminance.
I have an Eye One 2 Display device and the software is possibly similar in principal to that of the ColorMunki.
In Advanced mode I get the option to check contrast but I do always leave at native 50%.
The next stage is to set the RGB "gains" individually to set the colour temperature (6500K).
Next is the brightness adjustment and finally the profile is created.
If you use the basic mode, then the profile is usually created without you having to adjust brightness, contrast or RGB gains. This is often perfectly satisfactory because the calibration process produces a Look Up Table (LUT) for the graphics card to use to set all the colour values. I assume a mac is no different to a pc in this respect.
If I open the exact same tiff file in both Aperture and PSE9 and place both on the calibrated monitor, the images are different. Some colors subtly so but the Aperture reds are brown in PSE.
It sounds like the image colour space is not being recognised or there is a mismatch somewhere.
I don't know anything about Aperture - is it fully Colour management aware, does it automatically or allow you to set the monitor profile, how does it read the colour space of an image?
PS uses a working space, say Adobe RGB and "tags" the image with that. However, "correct" way for all CM applications to read an image colour space is to embed the profile in the image - you can embed with PS.
I hope that is some help but you really need a Mac expert to comment here.
Terry