Here's an odd one for you: something in ZOmnibus is affecting edits made to chat options by another add-on.
To be specific, Odyssey of The Summoner changes the dialog options at the Last Hope weapon merchants. In the... we'll call it a campaign, as that's effectively what it is... you play as a (presumably humanoid) spirit trapped in the body of Wilder Summoner's summoned being. As such, you are not able to learn standard techniques for wielding weapons and armor, i.e. Combat Training. To this end, the dialog options for 'Avatars' (said spirits trapped in animal bodies) are altered when talking to the merchants in Last Hope. You can ask them about training, but they cannot teach you (i.e. there's a silly replacement dialog).
When playing OoTS with ZOmnibus enabled, something
in ZOmnibus is adding the old chat options back
for these merchants, while still leaving in the replacement options. Not only does this look silly, but there is a very good reason that Avatars should not be able to learn Combat Training: none of them wear armor, and none of them wield weapons (with one 'unconventional' exception). They have mechanics in place to make up for this, so the ability to gain Thick Skin as well is not something they should have, though the other talents are largely irrelevant.
I poked around a bit in ZOmnibus, but I couldn't figure out what the cause might be. I would suspect Store Wishlist (you know, 'cause stores) but I'm not really sure why this would be affecting the chat options. OoTS is still very much in development, and the author has a lot on their plate with chasing down their own bugs and releasing more content. I have been using ZOmnibus nearly as long as I have been playing ToME, but I decided it would best to turn it off while playing OoTS after I realized it was the cause of this behavior and couldn't be sure what else it might be affecting. Since this is essentially an early testing release, I want my runs to be as 'clean' as possible and have limited the other add ons I use down to strictly QoL. ZOmnibus was most of my QoL, though, so now I'm down to just Faster RRE.
I understand that this is an inter-add-on conflict and might not be something that you can address, but I figured there's no harm in asking. OoTS is probably one of the only add-ons that modify these chats, but I assume you'd like ZOmnibus to avoid conflicts such as this, if at all possible. As OoTS is quite literally replacing the old dialog choices (as far as I can tell; their code is a bit more sophisticated than anything I could manage), it just seems really odd the the old dialog options are somehow getting worked back in. Anyway, thanks for your time. Cheers!
(P.S. If this is something you can look into, these modifications are handled in OoTS by the file chat_modify in the data directory, at line 480 (using a few functions defined at the top of the file). Unfortunately, that's about as much help as I can be