@Frank Apisa,
She asks for the number of wishes to be thought of in terms of its absolute value, so -1000 wishes count as 1000, because the absolute value of -1000 is 1000. When she wishes for her wish count to go down by 1000 at the end that takes her wish count from 0 to -1000. But the genie has already granted that -1000 wishes count as 1000, so she ends up with 1000 more wishes.
I haven't figured out why she had to make the first wish, though.