Notice the runtimes in thetvdb.com Some are 85 minutes. You may need to combine DVD episodes together to match what is in thetvdb.com.
Using aired order on thetvdb.com for season 2
e1 = Trials of the Heart, 85 minutes, possibly DVD e1 & e2 combined.
e2 = Heart & Soul = DVD e3
e3 = Heart’s Desire, 85 minutes, possibly DVD e4 & e5 combined.
e4 = Awakenings & Revelations = DVD e6
etc.
Unfortunately, the DVD order on thetvdb.com does not match your DVDs. If you set Plex to use DVD order you will still have to combine episodes, just in a different combination than the aired order.
You can use MKVToolNix to combine episodes before adding them to Plex, transcoding with Handbrake, etc.
