Yes, off course. I re-created some mods with the generator to test my hypothesis. When I select "Create Duchies" in "Create Options", and if a Kingdom is generated from a Titular Duchy generated from a County (like the Kingdom of Brescia of my first exemple, or the Kingdom of Troyes in a other mods), the Titular Duchy "where he comes from" is with the other "de jure" Duchy of the Kingdom, and when I reload the save (with the mod, of course), this particular Duchy become a "de jure" Duchy of the original vanilla Kingdom (Italy for Brescia, France for Troyes), the other Duchies remains "de jure" duchies of the Titular Kingdom. However the duchy remains under the control of its owner.
This never happens when I do not select the option "Create Duchies" in "Create Options". Titular Duchies always remains "de jure" of the created Kingdom after reload.
Sorry for my broken English.
I can't fix this problem. The De Jure liege of counties are not stored in a save game.
I've uploaded 1.6.5. In Full History with custom duchies, custom duchies will now always have a de jure liege, so it won't crash in the De Jure Kingdoms map mode. I've also changed the DefaultGains.txt file so it won't change the De Jure liege of counties when created a titular duchy. Because of this, the title will always be titular.
I think I've fixed the problem with the Pope being a vassal. At least, I couldn't find a generation where he was a vassal.