The monitor layout is stored with your window layout. This is so you can configure multiple PCs (with different monitors), and when you show your config to someone else, they can see your window layout as it was intended, rather than mashed across their own monitors.

To get the right screen size, use the drop-down that says "<Pre-defined Computer>", and select <Current Computer>. The next time you look at it, it will have reverted back to "Pre-defined Computer" (you defined it at the moment you set Current Computer).

Alternatively, you can always create a new window layout, and it will use your current monitor layout