I'm not sure if this is still a known bug or a solution was posted during the SEQ discussion.

I'm having issues with dialogue topics contained within non-SGE quests resetting after quitting Skyrim and relaunching the game. This affects all topics, including those marked with a "Say Once" flag and top-level comments (faded-out topics will return to their normal status).

Dialogue within SGE quests are not affected. Exiting to the main menu and loading the save again does not cause a reset.

I've also generated a new SEQ file and tested from a new, clean save, but the issue still persists.