HER2 positive because of COPY NUMBER??

My wife's initial needle biopsy came back HER2 positive by FISH testing. After surgery an IHC test read negative (+1), and the medical oncologist had another FISH test done which came back less than 2 (typically considered negative) but with a copy number of 6+. The medical oncologist informed us that according to the new 2013 guidelines she is considered HER2 positive based on the copy number.

Her tumor was 7mm IDC, surrounded by stage zero DCIS-no lymph node involvement. She is 52 years old and had an oncoplasty lumpectomy. She is also strongly estrogen +, and progesterone +.

We had several days during which we celebrated her new HER2 status before the second FISH test results.

This has been quite the little roller coaster ride and she is pretty upset tonight after believing for several days that she would not have to consider chemotherapy and Herceptin.

I guess we are a bit confused by all of this. I can see why having more than the normal two HER2 copies on the 17th chromosome would be HER2 positive, but am unclear as to why the ratio would be, or could be considered negative?

Has anyone else been diagnosed as HER2 positive based on copy numbers?

Thanks, we have read a lot here and gained quite a bit of knowledge as lurkers!