BINGO! Let the machine cool down, it wouldn't start (same symptoms as before). Opened up the case and checked both SATA cords, I noticed one of them was zip tied (Shuttle factory install) and the cord looked a little tight and pulling connector a tiny little bit to the left. Undid the zip, reattached with more room and restarted.
The machine started up properly immediately afterwards.
Will do some more testing to make sure this is it and not some other silly thing that got bumped when I was opening the cover. But looks like you solved the problem!