When “Fix pane height and use scrollbars” is checked, layout on a few of the old Pepper get thrown out of whack. The Feedburner panel, for example doesn’t stretch the table out 100% to fit the width of the container. Also, the Trends Pepper forces the header onto two lines cutting off the text below. They display fine when the setting is unchecked.
Not a big deal and may be resolved when the Pepper release specifically for v2 but thought it worth a mention.