After looking over your post, maybe because you are using free version? Did you minus entire SS amount or the SS tax amount? Procedure I used worked for me.
I minused the entire SS amount in both scenarios. What it did in the one case was subtract it from my pension income, which brought my taxes artificially too low.
In the case where I had put it in as SS income and then gone down to the misc income and entered the exact same amount as a negative number, it had already calculated a taxable portion of the SS and added it to my pension income. So when it then went to subtract the negative social security, it subtracted it from the combined pension/taxable portion. Still not the correct calculation, and an oddly high tax refund amount.
In both cases, the refund numbers did not match what I've gotten several times by doing it on paper. I'm playing it conservatively and sending it in with the manual calculations. If they surprise me with more than my calculated $207, I'll be pleased.
Perhaps it makes a difference as to how much taxable social security we are talking? I know that, depending on your other income, the amount of SS that is taxable changes. Perhaps your amount of SS was such that it was not taxable at all?
I did contact turbo tax and they say you can't do any override adjustments online, and you cannot e-file an overridden entry on the desktop version.