Could be lots of reasons. Is the amount on 1099R box 1 and 2a different? The taxable amount can be different by the amount in box 5. Like if you made an after tax contributions to the pension. That's what I did, when I retired I was able to buy back more time. So the plan keeps track of it and prorates it on the 1099R. You would have to ask the plan why the taxable amount is different.
