Library organization

[theguymadmax]

My movie directory in Jellyfin is E:\ and my shows directory is E:\Shows.

If the way you phrased that is how I'm interpreting it (that movies are in the E:\ drive without a sub-directory) then that's the issue.

Map your media using the below structure as a guide, then delete your libraries and recreate them with the new path.

Movie Library
E:\Media\Movies\
E:\Media\Videos\
E:\Media\DVD\

Shows Library
E:\Media\Shows\

Also, each show and movie should be in it's own folder within these folders, as stated documentation that TheDreadPirate linked. A screenshot of your folder structure with files would help if this doesn't immediately solve your issue.