Any issues around filling out a FormsCentral PDF, whether created in FormsCentral or an Import PDF, are 99% of the time due to not using Adobe Reader or Adobe Acrobat to fill out the PDF.
When you say "The forms that I downloaded to my desktop to send out manaully works fine." it makes me wonder if you are having users fill out the FormsCentral enabled PDF in a web browser as opposed to downloading and filling out in Adobe Reader on the desktop, we highly recommend that users download the PDF and fill it out in Reader rather than in a web browser where you have little control over which PDF viewer is used.
Make sure that users are filling out in Adobe Reader (available Free at get.adobe.com/reader/) or Adobe Acrobat to fill out and submit the form.
See these two related FAQ's and let me know if you don't think they answer your issues:
PDF in a Web Browser FAQ: http://forums.adobe.com/docs/DOC-4142
Why does the Submit not work in my PDF form FAQ: http://forums.adobe.com/docs/DOC-2653