Further update - on a whim, I had a manga by one of the same publishers as one of the publisher directories that wasn't ry showing up in the parent directory, but it wasn't in that directory at the time, so I moved it in there to see if it would show up, and I got a new message on the log:

20180906 05:48:44 [Scanner thread] WARN com.ubooquity.data.database.c - Could not find id of root path D:\Comics\Kadokawa Shoten (ignore this warning if you just added a new root directory)
20180906 05:48:44 [Scanner thread] WARN com.ubooquity.data.database.c - Could not find id of root path D:\Comics\Futabasha (ignore this warning if you just added a new root directory)
20180906 05:48:44 [Scanner thread] WARN com.ubooquity.data.database.c - Could not find id of root path D:\Comics\Shogakukan (ignore this warning if you just added a new root directory)

Further, a whole bunch of new books were shown as added in the status scene - but it's still not showing up in the library. The publisher directory is showing up - but at the same root level as "Comics", but without all the books that were in that directory. (:confused:)

Since the files still aren't being added to the library, do you need me to send you the filenames or copies of sample files?

Removed the exclamation point, re-scanned, and the directories for Kadokawa Shoten (the Fate manga), Shogakukan (Getter Robo), and Futabasha (Shin Getter Robo) still aren't showing up.

Follow up on this - I double checked the logs, and here's the errors that I found:

20180828 19:17:21 [Scanner thread] WARN com.ubooquity.data.database.c - Could not find id of root path D:\Comics\Fate Kaleid Liner Prisma Illya 2wei! (ignore this warning if you just added a new root directory)
20180828 19:17:21 [Scanner thread] WARN com.ubooquity.data.database.c - Could not find id of root path D:\Comics\Fate Kaleid Liner Prisma Illya Drei! (ignore this warning if you just added a new root directory)
20180828 19:17:21 [Scanner thread] INFO com.ubooquity.data.database.c - Inserting/updating comic entry in database : D:\Comics\Fate Kaleid Liner Prisma Illya 2wei!
20180828 19:17:21 [Scanner thread] WARN com.ubooquity.data.database.c - Could not find id of root path D:\Comics\Fate Kaleid Liner Prisma Illya Drei! (ignore this warning if you just added a new root directory)
20180828 19:17:21 [Scanner thread] WARN com.ubooquity.data.database.c - Could not find id of root path D:\Comics\Fate Kaleid Liner Prisma Illya Drei! (ignore this warning if you just added a new root directory)

However, that doesn't apply for all the relevant directories - the directories for two other comics are detected, but their contents don't show up in the library.

20180828 19:17:20 [Scanner thread] INFO com.ubooquity.data.database.c - Inserting/updating comic entry in database : D:\Comics\Shogakukan\Getter Robo (1974)

20180828 19:20:02 [Scanner thread] INFO com.ubooquity.data.database.c - Inserting/updating comic entry in database : D:\Comics\Futabasha\Shin Getter Robo (1996)

EDIT: One other note - I'm using Manga here, and I've noticed that manga chapters aren't consistently listed in ComicVine, so using the ComicVine scraper is not necessarily an option.