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The easiest way to clean your preferences is to hold down the Ctrl/Cmnd + Alt/Option + Shift key while launching AE. You'll get a warning as AE launches that says "Do you want to delete your preferences" or something like that. It's much easier than finding the file.
It looks like you've found the panel but for others, if you want to find the file to back it up before deleting it you should look in your User/Library/Application Support/Preferences folder on a Mac or Users\<username>\AppData\Roaming\Adobe\After Effects\ on a PC.
You edit the preferences file using the Preferences Panel. Check the help file to find out what's there. The list is too long to go into here.
Thanks for that info, I was just curious as to how that preference was generated. When I put them all (the MC preferences) in the trash and opened AE the interface is not scalable and the buttons to close, minimize or resize the window were hidden beneath the menu bar.
Ive been trying to learn about things in the computer, like where file are stored and what they are used for, so that I can trouble shoot without calling tech support.
The "MC" in that file stands for MediaCore, which is the umbrella name for technologies that are shared between Adobe video and audio applications (Premiere Pro, Audition, Encore, etc.). When you see "Initializing MediaCore" on the splash screen, it's referring to the same thing.
This particular file stores values you set in the After Effects preferences that are related to MediaCore audio/video functionality, such as Preferences > Audio Hardware and Audio Output Mapping.
This file doesn't have anything to do with the user interface, so it should not have caused a problem as you described with the application window controls. Other files in the preferences directory, such as the Workspace files, are related to that functionality but should not cause such a problem simply by removing them. I suspect some other factors (other files deleted, or doing so while AE was still running) contributed to the behavior.