So you have Level 2 = 'N/A' as your own calculated subtotal for all of Department of Agriculture? If that is the case then that is why the number doesn't match when you collapse up to the next hierarchy. I would remove your 'N/A' rows and just add a proper sub-total: Analysis > Totals > Subtotals. And if you want the total to appear on the top select 'Column totals to Top' as well.
Hi Trevor, thanks for your suggestion but I actually want the opposite of that. The N/A (or in this case subtotals) rows that appear after expanding are the numbers I want. When I collapse the rows, Tableau aggregates the percentages below by averaging them and that's what i don't want. I want to collapse the rows and have the N/A subtotals show as the correct numbers.