Can having iron deficiency cause a positive 1:640 on an ANA blood test?

No. I have never heard of this either.  I have a high ANA 1:1280 speckled and homogeno pattern.  It was thought I had Lupus, but later we found out I had Sjogrens Syndrome....which mock the symptoms of lupus and other disease easily.

I am surprised your Doc didn't refer you to a rhuematologist.  I would tell your Doctor to do that immediately.  If this is a rheumatologist that did the testing, then I would get a second opinion.

You know your body more than any Doctor.  If you are feeling this bad....definitely go to a specialist that deals with high ANA's, titers, etc.  
Hope you get back on the road of feeling better soon.

BTW- I have iron deficiency too.

No, your doctor is wrong.  An ANA is a non specific test for an auto immune disease...maybe he thinks you have hemolitic anemia...hopefully not as this would be terrible.  However, an ANA would not be associated with an iron deficiency, not in the least.

Your Lupus panel came back negative but that really doesn't mean too much.  Really the Lupus panel is used to rule Lupus IN, not OUT.  Only 30% of people with Lupus actually test positive for the Lupus panel.  This is why they say that there is no specific test for Lupus.  You should see the hemotologist and then ask to also be referred to a rheumatologist.  If your primary care doctor balks at this suggestion, let her know that if anything occurs as a result of his lack of attention then you're attorney will be calling her (this always gets the referral, by the way).  After you do this you'll have to put in a request with your insurance company to change primary care doctors, but who cares, she sounds like an idiot anyway.  

Get copies of all your lab work.  Ask the doctor for them (before you threaten her with a lawsuit).  Have them make a copy so you can actually view the results.  Approximately 5% of the population test positive for ANA even without an auto immune disease, however this is a small percentage, so odds are you have some type of auto immune disease.