When I was trying to watch my copy of Batman The Animated Series, I noticed that the episode order in Infuse was completely different from the actual episode that played. Looking at my file naming scheme, I found that all of the files were incorrectly named.
After more investigation, what I found was that my current file naming scheme and Infuse’s was based on TheTVDB’s “Aired Order” (http://thetvdb.com/index.php?tab=season&seriesid=76168&seasonid=9798&lid=7&order=aired) of episodes instead of the “DVD Order” (http://thetvdb.com/index.php?tab=season&seriesid=76168&seasonid=9798&lid=7&order=aired&order=dvd). After discovering this, I immediately fixed the file names of the episodes locally. However, despite fixing this and having Infuse re-evaluate these files, the episode order in Infuse still uses the Aired Order. I also tried to force Infuse to use the “local metadata” for the files, but that did not do anything because I do not have an nfo file for the episodes - only the file names.
It would be nice if Infuse allowed me to select the specific order of episodes for exceptional situations like these as I have never encountered this before.