The BootstrapCK-Skin is a skin for CKEditor based on Twitter Bootstrap styles.
Some things couldn't be changed inside the skin, like the smileys and the position of the browse buttons when inserting an image or a flash.
Here's how you fix that:
plugins > image > dialogs > image.js and to
plugins > flash > dialogs > flash.js
In both, change the margin-top to 17px (instead of 10px).