RichMM, I assume that your much larger IRA is indeed a traditional IRA, not some other type of retirement account.
"I have another much larger IRA with another company, so I answered with that amount, and in response TT reduced my tax refund by over $1000."
Yes, that other IRA must be included in the year-end balance that you enter into TurboTax.
"Now I understand that TT was assuming only a pro-rated fraction of the taxed funds were converted."
That's not an assumption, that's the result required by law.
"However, since at the first company the entire IRA was converted, 100% of the taxed funds were converted."
That is false. Only a pro-rated portion of your total balance in traditional IRAs was converted.
"Thus, the TT question is misleading."
The question seems quite clear that you must include the sum of the year-end balances of all of your traditional IRA accounts.
The portion of your basis in nondeductible traditional IRA contributions that was not included in this Roth conversion remains in your traditional IRAs to be distributed proportionately until you have no more money in traditional IRAs.
