After adding my second W2 form, the return amount from that form was not added to my total Federal Refund?

That is entirely possible.  Not only did you include withholding amounts from that W-2, but you also added taxable income to your return. 

The additional taxable income may have increased your income tax so that the withholding amount was used to cover the increase in income tax.

You should not rely on what the refund meter is doing until you have completed your entire return.  It is not possible to tell what is happening behind the scenes of your return by just looking at the refund meter.  Adding more income can cause changes to various credits and other calculations in your return.