To change the format of the default template, replace the installed template with one you prefer. Save your .pptx template file to C:\Program Files\SAS\JMP\12\pptx\JMPExportTemplate.pptx. The style (headers, footers, logos) and aspect ratio (e.g. 4:3 or 16:9) of that template will be the default for current reports saved to PowerPoint. You can also use this method to make your organization's template the default template used by JMP.
John Schroedl jschroedl, who helped develop the PowerPoint export, suggests that your PowerPoint template file should have a Table somewhere within it, for example, on the first slide. This lets JMP know the style to use for tables. If there is not a table in the template file, JMP's uses some defaults that may not display the way you want them. So make a table - no need for any data in it – on slide 1.