I created a work around for this that you might try.
When I receive one cheque paying for several invoices on different jobs I do this.
I have an "Undeposited Funds" account (current assets), where all my cheques received go until im ready to make a bank deposit.
When I get that one cheque thats paying for more than one job follow these steps:
1. Receive payments, enter the portion received for that job - do this for each amount, you will have several entries with the same cheque number. These go to "Undeposited Funds"
2. Make deposit, Set up a dummy account such as "multiple cheques bank account" and select those payments you just received on that one cheque and deposit them to that new dummy account.
3. Make transfer,
From: your new dummy account "multiple cheques bank account" / select all the funds that equal that one cheque
To: back into your undeposited funds account, but now it will show up as the total of the one cheque.
4. Make deposit, (this is to your regular bank account)
You will have all your other cheques and then you should see that one combined cheque you transfered over from the dummy account, you can manually add in the cheque # and any other details you want.
"make sure after you do your deposits that your dummy account is at a zero balance"
Hope this helps till they get it sorted, was so much easier in the Desktop Version