Thanks for the reply. Sorry what I meant was that on the amended return, Turbo Tax added in the 10% penalty in addition to the withholding on the 1099. So between the increase in tax due to increased income and the penalty I owed $832. $597 was paid on the 1099 so that leaves $235, which I paid.
Basically i received a refund of $1531 initially and then when i filed the amended return, it said I owed back $235, which I paid. Then in July I got a bill in the mail for $597 plus interest and penalties. I called the IRS and spoke to a lady who agreed it looked like there was an error but said processing was probably still going on and it will likely work itself out. She put my account on a 30 day hold. Then I got another notice saying I need to pay. When I looked up my amended return status online it says completed as of 7/12 so I don't think they're reviewing anything else. I sent off my amended return a few days late on 4/25, it was received by the IRS on 4/30.
As far I can tell i submitted the info correctly because thats how turbo tax calculated the $235 i had to pay. I've broken down the numbers using the tax table and as far as I can tell, I have paid and they did not account for that withholding on the 1099. i am just hoping they will acknowledge and respond to the letter i'm going to send. i'm not sure how else to alert them of the error since calling them apparently did not do the trick. Also the hold times are insane.
