It's rather irrelevant if your mods should or shouldn't mess with these quests. The simple fact is that a mod affecting X system can have effects it's not supposed to on Y system.
There are a few possibilities here.
- Whatever mods you are using, make sure they are updated to their latest version. In an ideal world, these new version were released after the latest game patch. If they have not, check every mod page to verify if issues have been reported on these individual mods. Note that no issues reported for a mod does not mean it is not causing issue when used in conjunction with another mod.
- Disabling mods through the launcher is not disabling mods entirely
. You can try manually deleting every mod you have installed but there is no certainty in doing that. The only
way to ensure a proper vanilla state is through a clean install as described here
. Note that this may not fix modded saves and may require starting over.
- You can also try looking for some console commands to use through CET to force it to happen. I can't tell you where to easily find it but theoretically, you could force almost any event through the console. The CET Discord would be able to give you more information on this if it's at all possible. Thing is, there is no telling what you may break in doing so and you might just be pushing back the issue and making it worse.