The royalty income is not being counted three times. However, it will be listed under the Personal tab and the Business tab.
A 1099-MISC for self-employed income can be entered under the Business tab, in the Business Income section under Business Income and Expenses.
A 1099-MISC can also be entered in the Other Common Income section under the Personal tab. If you enter it here TT will also generate a business return (Schedule C) if appropriate (as determined by your answers to the TT interview questions.)
You would not enter the same 1099-MISC into both places.
