(a) I got my Bane files from the following sites:http://www.oldgames.sk/en/games.php?article=216
http://www.classic-pc-games.com/pc/role_playing/wizardry_6:_bane_of_the_cosmic_forge.html
With both versions, I experienced the same issues, so I suspect that they are the exact same "data" (whether that is the issue or not).
I owned the original version back in the 90's, but those floppies are still stashed away somewhere at my parents' house. I also bought Ultimate Wizardry Archives a number of years after that, but lent the CD-rom to a friend. I don't mind buying such a great game again, but that would take some time and effort considering that I live in Japan, and I don't know if I will experience the same problem even with the legit version.
(b) I already inspected the files using MadGod's editor, and they seem normal. In the main level of the castle, I am only supposed to meet Rats 13.33% of the time, and Giant Rats 26.67% of the time. I am clearly supposedly to trigger the Queequeg incident in his appointed place as long as he is still alive, and the Captain Matey incident is located in its proper place. The encounter in the Belfry is set to be the specific monster "Vampire Bats" even though when I actually play the game rats keep popping out when I ring the bell.
I still suspect that the problem is not with the data files themselves, but with the way they are being processed (by DOSBox, or by the system files that come with the game).