Is this happening with fields that are on Master Page only or with all fields in the form?
Is it possible for you to upload a sample/test form that exhibits this behavior?
I'm having the same issue as well. In addition to the additions/deletions to the master pages, the signature panel indicates that a field on the title page of my form was filled in after validation. I ran a temporary script on the signature field's postSign event, using Acrobat's signatureGetModifications() method, to narrow down where the updates are occurring, and it seems that they're taking place either at the same time the signature is validated or just after. The form is set to automatically preserve scripting changes when it is saved; switching to "manual" doesn't help. Turning field locking on/off doesn't work, either. Once the form has been saved and reopened, though, the problem disappears and the signature validates correctly.
UPDATE 30 DEC 14: The master pages that are being "modified" have separate content areas for navigation buttons; it's these CAs, and their associated subforms and buttons, that Acrobat reports as being modified. I tried commenting out the scripts on the buttons' click events without success.
UPDATE 15 APR 15: I've compared the preSign version of the XML for the field that's being modified with the postSign version and found that the XML is somehow being modified by the act of signing the document. To clarify: I need to fill in a date field on my form to indicate when the form is closed out. I have the signature field's preSign set up to add the current date to the date field. The preSign XML includes <value> and <date> tags, which are missing from the postSign version. Why would applying a signature modify the form's XML?
After some experimentation, I've found that the problem seems to occur if there are subforms on a master page. Once I removed the offending subforms from my form, the signature validated correctly.