What you have experienced is not that out of ordinary if the process is not designed from the start. I have done a lot of large scale projects where many companies have been in charge of various aspects of the deployment. The only way a project of this type can be done is through lots and lots of discussions at the beginning. Programmers (& I am one) are typists. We can’t write a book but we can type it.
It is hard to find a great design firm that can do both design and programming. In most cases design firms will do the design and contract the programming to other firms, after all it is not easy to have programmers that know every programming language or CMS or server environment on payroll. At Click & Pledge we use several design firms simply to keep our design fresh and program the interfaces and sites ourselves. This approach ensures the design is fresh and we are confident the code is secure. Our site brought together 2 companies that did the design of the site and the Flash screens while working with our internal programming team to bring it all together. I will not do it any other way.