My money is still on the daughter wandering around or something and missing the boarding cut-off. It simply doesn't make sense that a gate agent would randomly boot some kid off a flight that apparently wasn't sold out.
That said, the timeline still doesn't make sense. The OP says the new boarding pass was issued before boarding, so it's not like this alleged technical issue was holding up the flight, which might explain why someone would be IDB'd* from a flight that wasn't sold out.
(* Using the term loosely; if the passenger wasn't formally checked in, it's probably not a true IDB situation.)