Category not working with Accounts Payable
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Assuming there is no corruption of the Quicken installation or the Quicken data, the only possibility I can think of is that the op is looking in the wrong date range.
In my test, I setup two Accounts Payable invoices (both in the same Quicken Accounts Payable account); each with its own category (and a Schedule C tax line item assigned), and each with its own Business Tag. I entered a payment transaction for each invoice, then ran a few Business reports: Reports > Business > Cash Flow; Reports > Business > Profit and Loss Statement; and Reports > Business > Schedule C-Profit or Loss from Business. All the reports I tested correctly displayed the two paid Accounts Payable invoice amounts, with the correct Business Tag.
In order to get the desired transactions in a report, the report has to have a date range that includes the transactions. And for Accounts Payable and Accounts Receivable transactions, the date range must take into account the "basis" the user is employing.
If the "accrual basis" is employed, the "income" (from Accounts Receivable) and the "expenses" (from Accounts Payable) will occur on the date of the invoice (and it does not matter whether the invoice has been paid or not).
If the "cash basis" is employed, the "income" (from Accounts Receivable) and the "expenses" (from Accounts Payable) will occur on the date the invoice was paid (the date of the Quicken payment transaction).
{The "category" of the income or expense is always determined by the category in the invoice.}