What monitor are you using and what connection (HDMI, DVI or VGA)..?
I'm with the others and is seems like a contrast issue either with the Mac Mini or the monitor, but the shade part is a little puzzling.
I might try a different Profile like Adobe RGB, Generic RGB or sRGB IEC61966-2.1 and then play around with the contrast and color settings on the monitor.
1. To get to the Generic Profiles, uncheck the box "Show profiles for this display only"
2. Select a different Profile from the list until you find the best one for your monitor
3. Then try adjusting the settings on your monitor.
Optionally you can keep trying to Calabrate... and saving different Profiles until your happy, but as you can see I have no less than 4 tries for my W2253 LG monitor and even then had to work on the monitor's contrast and color setting.
I've only had the mini for a week and don't want to return it incase it turns out to be a software issue and Apple release a fix.
As a temporary measure I'm using Gamma Control http://michelf.ca/projects/gamma-control/ and followed instructions from another forum http://forums.macrumors.com/showpost.php?p=16226080&postcount=11.
This has bought the colours back to acceptable level and I'm not getting that shadow effect as detailed in the original post.