I've only had two weird things happen to me on that fight and I can't be sure why either happened. First one was like your situation, sort of. After the last crystal was destroyed, the raid was ported to the normal spot with the exception of High Elf babe-form of the chaos chasing me down wailing on me. Why are the women are always chasing me...

lol and another time when the raid gets ported at the start, one character got ported wayyy the hell far away in an unused part of the zone.
So, if I had to guess, 30 seconds or so of letting the chaos chase you to the entrance and he would have poofed and the treasure chest spawned (with you having no way to get to it). Maybe something with the portal-to-location part of the fight script? *shrug*
I haven't been able to replicate either time, but every once in a while someone in the raid does something to cause a little bug like this to crop up. Sorry guys, I know how frustrating that must be. 99.9999% there and poof!