When the annuity was 1035-exchanged from company Y, company Y should have informed company X of the amount of your investment in the contract, and that's the amount that should be present in box 5. Box 5 should not include any amount of investment gain that was transferred in the exchange. Box 2a should show all of the investment gains, not just the gains while at company X, and should be the difference between the amount in box 1 and the amount in box 5.
If company X refuses to correct the Form 1099-R, you'll need to submit a corrected Form 1099-R (Form 4852) showing the correct amounts. Entering a substitute Form 1099-R prevents you from e-filing.
