No, it shouldn't and it is not counted twice. You see it on your income summary screen as total income, but the rollover is not included as your taxable income.
You may check this by looking at your form 1040. The
rollover from a 401K would be shown in Box 16a, Form 1040. If the entire amount
is rolled over (most often with Code "G" in Box 7 of the 1099-R), the
line 16b remains blank and the rollover would not be included in taxable
income. (Form 1040A line 12a and b). The IRA distribution will show on line 15b form 1040 (Form 1040A line 11b).
