I had 'Application Frame' selected in the Window menu. The new GUI of Illustrator and Photoshop is bad enough (flat Windows mess) without this little annoyance. Close Acrobat/Reader and all open web browser windows. If you've updated to the latest version of Adobe Reader/Acrobat and it hasn’t fixed the problem, you'll need to repair your Adobe installation. I figure that I'm missing something rather elementary. Check the Adobe website for detailed instructions. With CS6, I hit Command-W and the opaque application frame/workspace is still there and I can't seem to get it out of the way without using Control/Comman/M. In the Registry Editor, make a backup copy of the registry by choosing Registry > Export Registry File. Type regedit in the Open text field, and then click OK to start the Windows Registry Editor.
Command-W and Photoshop was out of the way. So to get rid of that annoying update program, one option is to carefully edit the registry. Then, I'd click on the program beneath to see the update occur.
If I tweak a graphic from Photoshop and then return to Illustrator or InDesign to see how the updated graphic will appear, my usual mode of doing so would be to hit 'Command-W' to close the Photoshop window/work environment/application frame - or whatever one calls it. Like most people, I work with most of the CS6 programs open at the same time. Would this help solve the following issue: