I've done this instance 4 times now, and while I've never encountered any problems with the first boss chest, the Boarding Party chest NEVER opens for my groups.
I've been trying to get the set, but I've only been able to get the chest and boots, since the legs are in the Boarding Party chest, I'm probably never gonna get them.
And yes, we've tried different orders, Jedi Counsular > JK, JK > Counsular, along with smuggler and troopers first, nothing worked.
did you tank...atleast the last guy...on the platform by the chest. Thats what solved the problem for my group.