Start by getting your IRS transcripts; get your tax return transcripts and your account transcript, which should show the penalties and interest being added to you account and the taxes being credited to your account.
If the math adds up, then you are just getting beaten by the interest and you need to pay more. The penalty is 0.5% per month and the interest is a variable APR around 3-4% per year, so the total could be 10% or more per year, compounded monthly. For every $1000 you owed, it will increase by more than $100 per year, if your refund is less than the new penalties and interest, the penalties and interest may be gaining on you faster than you pay it off, and you just need to pay more.
In the unlikely event that your refunds are not being applied to your tax due balance, you will have to call the IRS to straighten it out. You can also try calling the Taxpayer Advocate service.
https://www.irs.gov/taxpayer-advocate
