Well, the application system seems to have finally spit out all of my information, so all is well with the application. phew!
I am a little suspicious that there actually was a problem, but at least my desperate emails to my referees resulted in my delinquent reference to say "Oh, right, sorry, I will get right on that!" so now everything has been received by the University and hopefully the department can access the last reference today.
Geez, usually it is me who does things at the last minute, nice to finally have a situation where it wasn't my fault!