I've noticed that when I add my own custom text above the core page code (Confirmation page, for example) it loses the formatting. So when the confirmation displays during the order process, it's all jumbled together in one paragraph. How can I add text to the core pages without losing the formatting that is set in these Core pages?
I suggest that you remove MemberMouse from the equation by disabling our WordPress auto-paragraph functionality:
Once you've done this, you may consider using this plugin (http://wordpress.org/plugins/raw-html/) to control WordPress auto-paragraph functionality on a page by page basis.