Index ends after 999 entries

The reason that this happens it that this plugin uses a function that to correctly work it requires a parameter specifying the number of posts to display and put 999 as that parameter as it seemed a reasonable number.

If you want to change that go that go ot installed plugins section, press the edit button and in the post-category-index-generator/index.php file search for the number 999 and replace with the number of posts that you want to display.

Be careful, because displaying too many posts/categories might use too much server memory and give and error if the available memory is too low.