Actually, started my game over, and it seems that not clicking on the pyramid had nothing to do with it. I think it was because I went through all of Cyseal without going to the homestead ( except for the hall of heroes, and talking to Astarte, so I could recruit fellas ). I collected many stones, but never went there until after defeating B Rex. Also strangely, after defeating him the purple lock on the chest in his room did not disappear, which I remember happening on another playthrough. Zixzax just sits at the front of the hall, and no more portals/storyline progression.
