Chris,
Reader cannot send a completed PDF unless it is Reader Extended. Reader Extensions is a product that extends the functionality of Reader on a form by form basis. My bet is that you were submitting only the data before (which is allowed by native Reader), then changeed the submission to submit the complete PDF. This is what I suspect broke the Reader submissions. So you have two choices:
1. Add Reader Extensions to the form so that it is allowed to submit PDF. There are two ways to add this right to the form.
A) Open the form in Acrobat, Click on the Advanced/Extend Feautures in Adobe Reader. Follow the wizard. Now the rights are applied and it should work in Reader. Note that by licence agreement that this technique is restricted to a max of 500 users
B) Get a copy of LiveCycle Reader Extensions Server and apply the appropriate rights to the form to allow this. This technique does not restruct the usage but it is much more expensive.
2. Change the submission option to send xml and not PDF then you will not have to extend at all.
Make sense?