The order of entry of Forms 1099-R makes no difference. The treatment by TurboTax of a rollover is entirely isolated to the particular Form 1099-R being entered.
TurboTax only needs to ask what you did with the money if the code in box 7 of the Form 1099-R does not automatically indicate a direct rollover. The codes that indicate direct rollovers are codes G and H.
Certain distributions are not eligible for rollover and TurboTax knows not to ask about rollovers for these. These would be a distribution made from an inherited IRA to a non-spouse benefiary (Code 4 in box 7 without code G or H), any distribution that has a code other than code 1, 2, 7, M, J, T or Q in box 7, a distribution that you indicate was all RMD and any distribution that you explicitly indicate to TurboTax was from a nonqualified retirement plan.
