>The problem is that after I run the .PRG that is supposed to resequence the table. When I browse the table in the command window, the table is not resequenced. But if I resequence the table directly from the command window, then browse the table, the table is resequenced properly.

SET ORDER TO is temporary. It does not change the physical order of the table. Because you close the table with the USE command, you have lost the order.