All amounts reported in box 1 of a Form 1099-R are considered to be income, so TurboTax includes the amount in your total income summary to help show that you've entered the Form 1099-R. However, amounts rolled over from your traditional 401(k) account to a traditional IRA account are not taxable income and are excluded from Form 1040 line 4b. This nontaxable income has no effect on your AGI or anything else.
Check Form 1040 line 4b to see that the amount rolled over is not being included in income.