For some reason, those regions it failed to detect were stored in the atlas file with a trailing space character.
Removing the trailing space seems to fix it, but I'll show it to Nate and see how that space got there in the first place. It might be a sign of some other thing that needs fixing.
Thanks for reporting!
For now, if you have Notepad++, you can use the "Trim Trailing Space" function in the menu.
Otherwise, you can delete that space manually in your text editor of choice.
Windows' Notepad may not be ideal since it doesn't recognize the Unix End of Line character format. But most other decent text editors should work.
Do you have any idea why the extra space character might be there?
This warning will be added in a future version: