During an Immortal Empires N'kari campaign I ran into the same phenomena where after a certain point in the game I stopped getting any confederation dilemmas. In this campaign I wanted to make sure to confederate Sigvald and Azazel. At some point, Sigvald wiped out Valkia, but i didn't receive a confederation dilemma with Valkia. Wanting to avoid the same issue occurring when I eventually wiped out my two targets; I started trouble shooting and messing with settings using the mod configuration tool.

During this I changed the availability setting of defeated faction confederations from "Player & AI" to just "Player Only". The next turn after changing this setting, I received a confederation dilemma with Valkia (who at this point had been wiped out for over a dozen turns) as well as Be'lakor (I am not certain how long he was dead prior to this).

My priority settings for defeated faction confederations is Player at 1 and same race at 2. Despite my settings it seems the confederation gets stuck in a limbo of sorts when defeat confederations are allowed for both player and ai, after a certain point in the campaign.

The mod author said they couldn't replicate this phenomena in an earlier comment, so now I need to find the time to clear out my mods and maybe do some test campaigns to see what causes this behavior to happen. At least now, changing the restriction setting to "Player Only" seems to work as a band-aid fix for those that experience this issue. Have yet to see what happens after changing the setting back to "Player & AI" after I get the LLs I want.

*EDIT* I don't know why I didn't see this and put two and two together earlier. There is a setting with the mod called "AI Turn Delay" under the "Restrictions" category in the configuration tool. By default this option is set to 50 turns. From what I've seen from other comments, the issue of dilemmas not occurring, and faction defeated events not showing up, both occur on or after turn 50. Something with this setting is causing the issue. I played a campaign where i didn't touch the ai availability setting but did reduce the AI turn delay setting to turn 1. This campaign suffered no issue of defeated faction dilemmas and events failing to occur. At the moment it seems changing any setting in the restrictions category corrects/prevents the issue.