Let's say that I click on the screenshot app that comes bundled with Ubuntu 11.10, and then select "select area to grab" followed by drawing the desired area, the resulting screenshot that is captured is, too often, coated with an Ubuntu-coloured glaze.
For example, if I screencap this Ask Ubuntu website, the white areas (all area, in fact) will come out with an orange hue. I'll cancel and repeat the process until the result is correct.
Does my description help? If so, then any idea why it happens and how to fix it?
It sounds like you're seeing a race condition between the application redrawing after the orange selection mask is applied and the screen contents being captured. So I would suggest filing a bug report. Remember to say what desktop you're running (Unity 2D, Unity 3D, Gnome 3, etc) since the compositing features could affect the behaviour.
One work around would be to use one of the other two modes (whole screen or whole window), and crop the result with an image editor like Gimp afterwards. Since these modes do not involve you masking an area of the screen first, you shouldn't run into this problem.
Not sure how this happened but my prtSc button was no longer taking screenshots but when I went to Settings>Keyboard>Application Shortcuts and reset to defaults it worked for me Gnome 3.4.2