This is curious. Happening on latest Marketpress. So every time I edit the checkout page in any way I have to go re-select it in the Store settings and save. This has to be a bug surely? I have to be honest, set up wise I am not finding Marketpress 3 a good UX.
It still needs you to go looking for stuff, read stuff, set up stuff, all outside of the setup. Flexibility is great but not at the expense of simplicity. It really needs to be at a much higher level than this to be adopted further. Otherwise very promissing.