I just added in a bunch of our audio, made a few changes to some quest and merged them into our ESM. I created a new seq file for this esm, and placed it in the SEQ folder. (Also tried creating one with TES5Edit). There is an ESP now where I did the same thing since I haven't merged it in yet.

The quest no longer auto starts, it used to. Also NPC's wont talk even if I advance the quest through console. That makes me think it has to do with the SEQ file, but it's there...

Does anyone have any thoughts about what I may be missing or need to do?

Thank you!

Same thing happened to a mod I was working on, no longer starts either. Not sure what caused it though.

Are you testing from a save that has never 'seen' your quest? If not, that could be your issue, since merging plugins changes formIDs.