We have also been having the same issues for months now, I have to send some manually outside of the system which just doesn't look as professional 

Its not until we are chasing for payment that we then know they haven't received an invoice, or they receive the same invoice multiple times. 

This is a basic procedure for an accounts package and I'm god smacked they still haven't managed to sort it! You need new developers as they don't seem to be able to do anything correctly or within a decent time frame.

We are also looking into a new accounts package as QB just isn't up to scratch with most of the others now.