So I didn't run into this problem at all with my first game. But this time around I've got an ini with more variables in it. Not sure if that is causing the problem, but here's the issue.
When the player completes a stage that stage's item value in the INI is set to 1.
On the stage select screen, that stage's icon calls on that item value and sets it to one of it's alterable values. If set to 1 the stage shows "complete".
The problem I'm having is that sometimes it doesn't seem to be writing the ini at the end of the level. I get back to the stage select and it's still showing up as incomplete. If I play the level several more times, it will eventually show up as cleared. There seems to be no rhyme or reason to why it works sometimes, and doesn't other times.
I've now set it to change the ini in multiple situations. First, when the player passes the goal post, it sets the ini value to 1. Then, in the event that triggers the fade out, I've duplicated the action. I still run into the problem.