On a fresh install of WordPress with Twenty Eleven as the theme, I created 3 post, and placed them each in two different categories. My ideal outcome would to to have post that are in more than one category be able to be sorted independently in each category. I created 2 sections in My Post Order named after the 2 categories, with each of the 3 posts in both sections. I sorted the posts in different orders in each section, and it had no effect on the post order in the categories.
Okay, so this plugin can't do complex sorting, that's okay.
Next, I deleted the second category from WordPress and the second section in My Post Order. So now I had 1 category and 1 corresponding section. I still could not produce any change in the post order.
Finally, I deleted the other category and section leaving no categories and no sections, just three post.
I sorted the post individually in My Post Order and it still did not change the order of the posts on the blog page.
The post maintained the default reverse chronological order no matter what I did with this plugin.