Roku media Player indexing issue

JLarson 

Looks pretty good to me and yours is similar to mine. (not sure if you have a typo in message or are using E and e in your files names, though.  These may be being seen by RMP as different naming schemes).

I organize everything into files and add a few extra digits in my file naming schemes.  In the below example, assume I have a show called "alpha" and 3 seasons.  For simplicity sake, 3 episodes per seasons.  I create 4 folders in all.

Folder 1 --> alpha

Folder 2 --> alpha_season001

                     S01E01.mkv

                     S01E02.mkv

                     S01E03.mkv

Folder 3 --> alpha_season002

                     S02E01.mkv

                     S02E02.mkv

                     S02E03.mkv

Folder 4 --> alpha_season003

                     S03E01.mkv

                     S03E02.mkv

                     S03E03.mkv

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I normally add the episode title so S03E03.mkv would actually be S03E03_episodetitle.mkv but you don't need the episodetitle as the S03E03 is the actual title.

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Now, what I have noticed with RMP is that any "metadata" you may have in the "Title" field will mess up RMP's ability to recognize your naming scheme.  It will instead use the file's metadata when organizing/listing the files. (ie. even though my file is named S03E03.mkv, the metadata Title tag may be showing "season3alphaepisode3" which is then throwing off my alphabetical order when in a list).

Try using a metadata editor (or tag editor) to view your mkv file's metadata and either Remove or Rename the Title Field to match the file name scheme you are using. (I usually just remove the title).  I use kid3 for Linux, so not familiar with the ones for Windows. (I think you can also use VLC under the Tools/Media Information to look at metadata as well, but not sure if you can actually Edit it.  There used to be a bug with the ability to Save changes to the metadata in VLC and not sure if ever addressed). 

I would start by checking the metadata and see if that may be your issue.