I have the same screenshot problem in Mint 13 x64 with Cinnamon. If this bug is the same issue, then it appears, "This is caused by AMD's proprietary driver. There's nothing [Ubuntu] can do about it."
Not sure what driver version, but I installed it from the package repos, not from AMD. Here's a workaround I just found that has worked for several screenshots in a row: switch to a text-mode virtual terminal (Ctrl-Alt-F1 on my system), then back to X11 (Alt-F8 or maybe F7/F9). If I take the screenshot right after that, I get the correct screen contents. Once I switch windows or something, it seems pretty reliable that I get old contents.
If it makes a difference, I was using Ctrl-Shift-PrtScreen (allows you to select an area to crop to, and copies to the clipboard instead of to a file) for most tests, but just verified PrtScreen alone seems to also work with this.