Did they take any tax withholding out of it? If they did you need to replace the withholding when you put it back or the withholding becomes a distribution and possibly have a 10% early withdrawal penalty. What code is in box 7?
If you are looking at a summary screen or review screen those show the full amount as income and lump a lot of stuff together. You need to check the actual 1040 form and make sure it's right. Check line 5b for any taxable amounts. For a rollover line b should be zero and the word Rollover by it.
After you entered the 1099R did it ask what you did with it? Pick you moved the money to another account even if you put it back into the same account. Then that will expand and you pick I rolled over all this money. Then it will expand to enter how much you rolled over.
