Retirement tax questions

So, should I do  the 1099R the way it SHOULD have been done? It is still taxing me on the full amount of conversion, not the amount I put in line 2a of the 1099R, the taxable amount.  The after tax portion, co-mingled in this account was documented on previous tax returns and 8606's and I provided to TD Ameritrade, but they wouldn't correct the 1099