System Preferences Window Cutoff

It will turn out to be a system caching issue, I'm sure.
AFAIK, the file com.apple.systempreferences.plist should be the file that stores the position settings for the app window.
It can take several attempts at removing that file (restarting each time) until the caching should correct itself.

You could also try one of the specialist maintenance apps that offer to do deep cache cleaning/resets.
OnyX is one, or ElCapitan Cache Cleaner, etc.
Another possibility - and if this remains totally annoying to you, that an OS X reinstall will fix.
 
Then, finally, it's a weird setting for your Spaces. You would need to reset Spaces. It's part of your local user account settings, but could be system-wide (not sure about that)
I don't know how to reset the spaces to defaults, but should help by clearing system caches (seems like I say that a lot :D )
A deep cache cleaning might do the trick. Keep in mind that a deep cache cleaning might affect other things - hard to say what until you try it.

If you log in to ANOTHER user account, do you still get the same off-the-screen System Preferences?
 
Maybe it might be a bug in the Finder from a third party app. So follow the steps in blog post Reset Macintosh OS X Finder Issues. See if that help.

Another step is house the Terminal app command:
Code: 
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -kill -r -domain local -domain system -domain user

Run that and wait for the Finder preferences to reset because in will take a minute for the Finder reset.
 
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