You're correct, KHave.
You'll need to create the transaction first. Then, receive the payment.
Have you tried changing the sales tax settings from the preferences? If not, here are the steps:
If the settings are correct, you'll want to run a Verify Data Utility tool to check for data errors. Just press File, Utilities, and then Verify Data.
If prompted, click Rebuild Data or go to File, Utilities, and then Rebuild Data.
If there's anything I can help you, please don't hesitate to comment below.