From TechGeekandMore (LINK: http://www.techgeekandmore.com/2010/02/14/apple-itunes-compatibilit...)
In the past couple of days, I have received may requests for help concerning another iTunes issue. It seems that on some iTunes installs, that when you start iTunes you get a message
"iTunes.exe has been set to run in compatibility mode for an older version of Windows.
For best result, turn off compatibility mode of iTunes before you open it."
If you click ok on the message then iTunes opens just fine and works, but seeing that message every time is just an annoyance that just shouldn’t be there. The solution offered by Apple (LINK: http://support.apple.com/kb/TS1489) is
Try these steps to turn Windows compatibility mode off:
However, as many of the requests for help have said the Apple solution does NOT work for everyone. For those, who still have issues after following the Apple solution, the I have a fix for you.
NOTE: THE SOLUTION WILL INVOLVE A CHANGE TO THE WINDOWS REGISTRY. FOLLOW THESE INSTRUCTIONS EXACTLY AND DO NOT MAKE ANY OTHER CHANGES TO YOUR REGISTRY UNLESS YOU KNOW EXACTLY WHAT THOSE CHANGES WILL DO. THE REGISTRY CONTROLS WHAT YOUR PC DOES. ANY UNNESSESARY CHANGES COULD BREAK YOUR MACHINE. THIS IS YOUR WARNING. Now with that said on to the solution.
***Note that there are also sections for Windows, WindowsNT, Windows Mail, etc, so make sure you are looking under Windows NT (You can also verify at the bottom).
Once that is done, close the registry editor and start iTunes, and you should no longer see that message.