Glenn,
Offhand I'd say that although obviously there is a problem, it's not fuse related. After all, the original FNQ-6 did blow and so did its FLQ-6 replacement. I assume this chiller feeder is single-phase 208v. taken off of a 208/120 wye secondary. If this were three phase, I would immediately suspect one of the phases....hang a clamp-on and look for overload, imbalance, etc.