I get that problem A LOT! Today it seems especially bad, but there are many days it has issues w/me. One day it wouldn't send any of my messages, had 4 people trying to have convos with me, thought I was ignoring them cause I was mad at them or something - NOT true at ALL! Damn facebook is ruining my social life! jk, got things sorted out within a couple days but STILL....
As for an explanation, all I've got is maybe Facebook people aren't too good at making a good chat program, and they must be trying to fix it but maybe they're just incompetent and don't care enough to put more effort into it