Thanks for your questions and answers. 1) the option in the company profile to consolidate is still checked - that is what confused me 2) I was only expecting to consolidate because that is what I was told to do when I was shown how to use the program.
The thing that was annoying me most is that all of these transactions show up on the detailed Trial Balance and it is getting longer and longer. It previously did not show any invoices to which payments had been applied and no longer had a balance owing. Any idea what has caused that.