I'm not saying it's plex it's fault. Since you point plex (which i also use myself btw) to the converted file (mp4), it's not plex's fault. That would only have applied if you were pointing it to the AnyDVD rip itself. Why just those 2, maybe those are your only 2 discs that have screenpass protection, that's the whole point of the protection. To scramble the scene order under numerous playlist files. If you have problems with certain DVD's, then you need to post those in the DVD section. The fact that UBRC doesn't show multiple playlist is of no concern or fault of anydvd. You'll have to ask it's developers how you can manually point it to a certain playlist, IF it supports that at all
And yes, anydvd does remove screenpass IF the title is supported by it (or to be precise, the online protection database), which in your case it is. Which is why the status window mentions "Java protected good playlists: xxx".
Paid software that supports anydvd's playlist mentioning: Elaborate Byte's "CloneBD" (will show all good playlists and will auto-hide bad ones, and also allows you to select a playlist yourself from those shown)
Free software that supports AnyDVD's playlist mentioning: Jdobbs's "BD-Rebuilder" (available at doom9.org, does rely on a few helper aps, but also lets you manually load a playlist too)
I use both tools mentioned above myself, depending on the usecase scenario i need it for.