I created a template repeater the exact size that I need (see the scroll bar) and included the headings on the main window with the template repeater below it. But when I publish the window it resizes the template to be smaller than what I originally set it up as. You can see how the headings fit the size of the template with where the scrollbar is, but the inside is shrunk where the heading no longer fit. For reference, in the designer everything fits perfectly.
Have you examined the layout properties of your components and templates? By default, Vision components rescale in a real client, and small pixel differences (including banners and docks) will screw up any pixel-based alignment.
Some pixel-based alignment can be made with "anchored" layout in place of the default "relative" layout. Sorry, complex combinations.
Your headers are outside of the repeater? Is the template a row or a column?