Hi @LawOfAardvark73,
Welcome in the Community !
The ordering of the level is by default done in alphanumeric order, which is why JMP gives you the calculated difference as Before minus After. To specify the ordering of the level, you can add the column property Value Order to specify that level "Before" comes before level "After".
Adding this column property should give you the test result directly in the right expected order.
Hope this answer will help you,
Victor GUILLER
"It is not unusual for a well-designed experiment to analyze itself" (Box, Hunter and Hunter)