Net investment income tax on cash from a partial 1031 exchange?

If the rental rises to the level of a Trade or Business AND you Materially Participate in that business, the capital gain is not subject to NIIT.

If that does not apply, the capital gain is subject to NIIT.

I suspect that TurboTax automatically assumes it is NOT a Trade or Business, and therefore subject to NIIT.

As for why your prior transaction did that, I don't know.  Maybe your income was not high enough to be subject to NIIT.  Maybe you used a different program.  Maybe I am wrong and TurboTax does have the capability to exclude it from NIIT and you entered it differently.  Maybe something else.