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

Resolution

Try these steps to turn Windows compatibility mode off:

1. Quit iTunes.
2. Windows XP and Windows 2000: On the Start menu, click My Computer (or double-click My Computer on the Desktop).
   Windows Vista and Windows 7: On the Start menu, click Computer.
3. In My Computer, open the C:\ drive (or whichever disk your Windows is installed on).
4. Open the Program Files folder or "Program Files (x86)" if you are using a 64-bit version of Windows Vista or Windows 7).
5. Open the iTunes folder.
6. Right-click on the iTunes application (iTunes or iTunes.exe) and from the shortcut menu, click Properties.
7. Click the Compatibility tab.
8. Deselect the checkbox under Compatibility mode if it’s selected.
9. Click OK.
10. Open iTunes and play a song.

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.

• Go to start –> run –> regedit
• When the registry opens go to HKEY_CURRENT_USER\Software\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers

***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 you are on the Layers section, look at the Window on the right and you will see a software key that says iTunes.exe. Delete that key by right clicking on it and then selecting delete. (Your key may look a little different depending on where you installed iTunes).

Once that is done, close the registry editor and start iTunes, and you should no longer see that message.