My taxes changed from an almost $700 refund to over $700 payment after putting in my stimulus information. Was the stimulus not tax free?

My understanding is that the stimulus was an "Advance" on your refund.  So it is quite possible that you were refunded more than you were going to get. 

The stimulus was tax free.  The program has a refund tracker that is designed to show your refund as you go.  It always starts with the maximum refund - which in this case assumes that you didn't get the third stimulus and are going to add it to your refund.  When you told it "I already got it" it removed the stimulus payment from your refund, changing it by $1400.