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The reason this is happening is because the default CSS for adminhtml has been changed a bit.
You can either replace the CSS from your default admin to your custom admin, and re-do the changes. Or, you can just probably add the following to your css to fix this.
Keep in mind that there are a few more changes in other sections. For instance, if you look at the payment methods section under configuration, you’ll see that the way the buttons work under paypal payments are different, and must use the proper styles to look and function properly.