I have MP installed on a single site, fully up-to-date. The shopping cart seems to work OK as a sidebar widget but the checkout spreads over a wider area and with the Checkout Now button being moved to within the main area.
I haven't set the gateways up yet - just selected manual payment and Paypal but I wouldn't have thought that would make a lot of different. The theme is gogotheme's Corporate and the site is f2khealthandfitness.com - go to Shop and select a couple of items say from the Run Products drop-down and go to checkout.
Can you see what is going wrong? Is there something not set?