Without the form it is impossible to know for sure, so I'll give you an idea to troubleshoot the issue.
1. Open the form. Set the fields in such a way that the conditional formatting 'kicks in'.
2. Save the XML to your machine.
3. Submit the form.
4. Reopen the document and save the XML to your machine.
Then compare the XML pre and post submission to see if there are any clues. Good luck.