So I fixed my problem in case anyone runs into this.
The problem was the Jamba quest log helper would not select quests for the group for abandoning and marking. CT_Mod (CT_Core specifically) was conflicting with this. I had enabled the "show quest level in quest log" option. As soon as I disabled that it worked again. I didn't want to have to disable CT_Core, but disabling the quest levels made it work again. QuestHelper shows the levels in its log anyway, so it's fine.
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