Yeah that was the problem I was told about if you don't send all the documents off together and send it without all the Police Clearances. Apparently, you now need to wait until they send you your letter of confirmation that includes the barcode stickers in it and send off the additional information with the barcodes on the outside of the envelopes so that they all match up when they get to the Embassy.
From what I was told, sometimes they don't always send the confirmation straight away, and you may need to wait until they request the missing police record and when they send you through the letter requesting it they will give you a three month window to send it in, and they then don't look at your application again until after those additional three months have passed, even if you send in the police certificate the next day.
I know this all sounds awful, and it was really hard for me to have everything sitting here ready to go and waiting the extra 6 weeks for my Australian Police Certificate, but all you can do is wait for the letter with the barcode stickers in, or your police certificate may not get to your file, then that would be a double waste.
You could always cross your fingers that they don't wait the whole 3 months, and this might be completely wrong, but so many people gave me this advice, I had no option but to take it.
Good luck to you.