Thanks Aquinas, that was very helpful. I think I can create a workaround for those who suffer the bug. It'll mean that all secret doors will be revealed, but it's better than the opposite. I'll make it so that the player has to explicitly ask Jaroo to activate this script.
Yes, in 8.1.0. In his dialogue, ask for healing, then say 'I have contracted a strange affliction while adventuring', it should be there, along with the particle removal treatment. Note that the condition for that dialogue line is game.story_state >= 1, which IIRC means you need to have learned about the moathouse.
I just had a problem that seems a bit different. I had been to the moathouse and cleared the top level. The secret doors where the Bandit Boss hangs out appeared. After that I went back to Hommlet without venturing lower; the entire upper level of Moathouse was cleared. After selling gear, I went to Welk and finished clearing it. Then I went to Hommlet, sold gear, rested, and went back to Moathouse. When I entered, the secret doors in the bandit lair were still there, I went downstairs to the zombies. Fought and killed them, got the magic chest, and then went to the torture chamber with the last zombie and killed it. That secret door with the stairs was also there. I went upstairs and rested in the tower. When I came back, the door to the secret stairs would open but the stairs were not glowing blue they were just gray. I went back to a save before I took gear from Welk to Hommlet, stashed gear in the chest in the Moathouse tower, and cleared the zombies. I immediately went to the stair and it was there and it worked. Cleared the ghouls and the crab and came back up to the tower So it seems, I have a different problem. It is not that secret doors do not appear at all or are unfindable, it is that some of them (all of them?) do not appear after you have found them once and left the area. ADDIT: Ah nvm, on my "chest problem" I had forgot it needs to be identified *doh* Then I noticed a slightly different problem different from what I've previously encountered: there was not command in the radial manu to activate the mini magic chest. Maybe I don't remember how it works right, but I seem to recall that all you had to do was have it in inventory and it would create a radial menu option to use it?