Index fund in both Taxable and IRA accounts, category report shows taxable income in both.

Is the IRA account coded as such in account settings? If so, this will prevent any income from appear in the Tax Report.

For a Category report of taxable income, I'd simply click Edit, click on the Accounts tab, click the radio button for Selected Accounts, and then de-select any retirement accounts. (The report is capable of to including income from retirement accounts because in other cases, you might want to see how much your retirement accounts have earned.)