NOTE: disabled and REMOVED is two different things ... so be sure once things are running happily that on all Modules for Shipping, Payment and Order Total that you only have INSTALLED the ones you actually use and that you click on the ones you are not using and make sure that you have REMOVED them ...

NOTE: also on Sort Orders on Modules make sure that they are all unique values or all set to 0 ... this holds true for everything except the Order Total modules where those must have proper Sort Orders to calculate correctly ...