If tax is due you will pay interest and penalty. Interest is about 1/2 per cent per month and penalty is also about 1/2 percent per month.

In my case.. last year I filed 1040 from a tax consultant and then refiled 1040nr. But I noticed majority of people file 1040. I am also planing on filing 1040 this year. What are my risks? Does this affect H1b visa processing?

To be honest, it probably will NOT affect your H-1B visa request, because the USCIS does not investigate the H-1B visa application too thoroughly.

When it WILL affect the process is when you apply for the green card. Then, they specifically ask about your tax filing status, and then they have the IRS back-check the returns filed. That is when the IRS will find out you filed incorrectly, and the USCIS will mandate that you amend the returns before granting the green card.

That could happen 5-10 years from now, and the accrued penalties and interest could EASILY double the additional tax due, which is why it behooves you correct the problem now while the additional tax is manageable.