The IRA box being checked is an obvious error on the 1099-R. A 401(k) distribution can NEVER have that box checked because a 401(k) is NOT an IRA.
IF you specified to the 401(k) plan administrator that the money was to go to a Roth and they put a 0 (zero) in box 2a then that is also an error on the 1099-R. However, if YOU changed your mind and deposited it into a Roth instead of a Traditional IRA that the check was made out to, then that was your error.
You should attempt to get the 401(k) plan administrator issue a new 1099-R (they should because of the IRA box) and put the taxable amount in box 2a which would be the same amount as box 1 unless you had any after-tax contribution in the 401(k) which is unlikely.
If they will not change it then prepare a substitute 1099-R (a 4852 form). Enter the same box 1 amount in box 1 and box 2a, a code G in box 7, do NOT check the IRA box. The interview will ask of it was rolled into a 401(k) Roth - say no, then it will ask if it was rolled in to a Roth IRA - say yes.
Enter an explanation why you are using a 4852 - say the 401(k) was rolled to a Roth IRA so the box 2a amount was not correct and the IRA box should not have been checked. Also state your efforts to get the 401(k) administrator to issue a corrected 1099-R.
You can choose a substitute 1099-R on the first 1099-R interview screen.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**