Thank you all for your replies.
I have looked into the situation and found that code signing can solve some of the false positives, sometimes. Code signing provides certainty of the source of the software, but not what the software does. So it makes sense that anti virus scanners don't see signed code as safe by default.
We will likely go with the code signed route anyway because it's a professional approach and it may help.
For the whitelisting however I understand that our software will need to be uploaded and analyzed. As you can imagine, management isn't very keen on this idea. I noticed on another antivirus vendor site that they mention that they can sign an NDA. I have read through the links you provided but I did not see the same offered by Symantec. Does Symantec offer the NDA option when submitting files for whitelisting? This would help put management concerns to rest.
Thank you for the assistance so far.