Penalties are based on your prior years' taxes. If you owed $3,000 last year and then you owe $3,000 again this year then you're going to get charged a penalty. The IRS sees that as money that you should have paid in estimated payments because - since you owed it last year - you should have known that you would owe it again. And they expect to be paid not when your tax return is due but when you earn the money just like with withholding from a paycheck.
So if you owed last year and then owe again this year - no matter what revenue stream caused you to owe the money - there will be a penalty generated by the system.
@Rockpowwer
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