I figured out what was going on with the 1099-SA. I started a new return and just entered my W-2 information. As I entered the information when I put in data in boxes 1-11, my refund showed a $4000 refund (fake numbers for illustration only). As soon as I put in the "W" code in box 12, the refund dropped to $3000 (again, for illustration purposes only). I finished up the W-2 and went immediately to the Deductions section and went through the medical questions which includes HSA questions. I put in the amount from the 1099-SA ($1775) and my refund dropped by about $750. However, the next question is "did you use this all for medical" and as soon as I answered "Yes", then my refund went back up by $750. As soon as I finished answer questions about "did you have an HSA family plan" and so forth, I noticed the refund amount went back from the $3000 to the original $4000.
So, the moral of the story is that I did not double count the "$5049.98 for code "W". However, I just did not realize that when the W-2 was entered (as I downloaded it and it was entered automatically when I asked the initial question) that TurboTax does not give you credit for the "W" amount off your taxes UNTIL you answer the deductions section on medical and give all the HSA information.
Moral of the story, ignore the refund part as it changes because TurboTax is doing stuff in the background that can confuse you. Problem solved, thanks for the replies.
