Are you looking at the Summary screen? This will show total income received but not the rollover. You need to look at your actual tax return, Form 1040.
Depending on the type of account that you rolled over the word ROLLOVER will be shown on enter Line 4b or 5b and there will be a 0 entered as the taxable amount on either 4b or 5b.
Click on Tax Tools on the left side of the online program screen. Click on Tools. Click on View Tax Summary. Click on Preview my 1040 on the left side of the screen.