I also have experienced the same problem.
After I had this problem, I connected Neo to PC,
started NeoEdit, and then reverted the config
on Pronto to factory default settings. Ant the I
immediately downloaded the same ncf file I did earlier
and then evrything is fine.

I am not sure either if I have to return/replace this.

But I am really having trouble making Neo learn some
keys from Yamaha rempote. Other devices/remotes were
just fine. So I suppose this is a problem with Yamaha.
Did you notice a problem in learning as well?