It sounds like you may have accidentally zoomed the entire screen on your Mac Pro, which is causing some items to be hidden.
OS X, particularly recent versions of the operating system, do a good job of corralling application windows by either not allowing a user to resize a window beyond the boundaries of the screen or by automatically snapping a window to a second display for those with multi-monitor setups. But sometimes — due to errors, bugs, or when disconnecting an external monitor — an application window can get “stuck” partially or completely outside of the visible area of the Mac’s display, and getting it back can seem impossible. Thankfully, there’s a quick and easy step you can take to automatically fix an off screen window in Mac OS X, and it’s called Zoom.
The Zoom function has long been present in OS X, and it’s normally accessed by clicking the green button in the top-left portion of a window (note, however, that in OS X Yosemite the green Zoom button now takes an application into, but you can still use the Zoom function by while clicking). This Safari window is stuck off screen, with its zoom button inaccessible. If you can see the green zoom button, it’s the best way to bring the missing portions of your OS X application window back into view. But what if it’s the top of the window that’s off screen, and you can’t see the zoom button at all? In that case, you can achieve the same result via an option in the menu bar. Simply select your desired application to make it active by click on its icon in the Dock (you should see the application’s name in the top-left corner of your OS X Menu Bar, next to the Apple logo).
Then, also in the Menu Bar, click the word Window and then Zoom. If you have multiple windows open in the same application, you can also select Zoom All to bring them all to the correct position at once. As you can likely guess from its name, this has the exact same effect as the green zoom button, and your partially missing window or windows will now be automatically repositioned and resized to fit your current monitor.
So the next time you unplug your external monitor and end up with a full or partial off screen window, don’t panic. Just remember Window Zoom to bring your missing application windows back. Want news and tips from TekRevue delivered directly to your inbox?
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John Manly's answer works for Adobe CC as of the 2014 update. Sadly that option doesn't exist in pre-CC and it sounds like Adobe have no plans to fix this. If you're on CS6 on Windows, there's a hack described here which works on Windows 7 and 8.
Warning: it involves hacking the registry, to enable 'external manifests'. Here's the link: It allows you to make AI and PS auto-scale with everything else according to your Control Panel Appearance and Personalization Display settings. Be aware, however, that this makes everything, including the appearance of your artwork, slightly grainy as if it was a pixel image that had been scaled up, and that the same Windows scaling applies to Adobe stuff as everything else including web browser etc. After trying every possible combination of settings, for me they all either scaled Adobe too much or everything else too little, or both, and I ended up undoing all of this and simply turning the resolution down one notch. But it might be an option for people with different personal preferences. Here are the key steps.
Before editing the registry, I recommend reading that whole article, and the comments. Here is instructions for older versions of adobe products (before CS6). Follow the instructions above by user568458 (make sure you can view the file extensions). If you try to open the program you will get a dll error. Here is how you fix it. Look in the folder where you placed the manifest you will see a different.manifest file.
For photoshop CS4 it's Microsoft.VC80.CRT.manifest. Open that file, it contains a line which starts.