Where are you looking? 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 your return and make sure it's right.
For 1099R check the actual 1040 line 15b or 16b for any taxable amount. If it was a rollover it should say ROLLOVER by the "b" line. (1040A lines 11b & 12b)
Then you should not fill in box 2a. You enter the 1099R exactly as shown and answer the follow up questions to determine the taxable amount. Leave 2a BLANK.
