Why is that when send a customer an invoice with the deposit for a job the new total balance that’s due is less than the actual total ?

Let me elaborate in detail on why the new total balance differs from the actual total, scottsprimelands.

Normally, the new total balance is less than the actual cost if deposits are turned on the Sales form content section. I've attached a screenshot for your visual guide:

Once turned on, if deposits or payments are entered on the invoice, this will deduct the amount from the actual cost which is the Subtotal, and will generate a new total balance or the balance due. Please see below:

You'll want to turn off the deposit feature on your invoice so you would come up with only one total balance. To do this, follow the steps below:

1. Click the Gear icon, then Accounts and settings.
2. Go to Sales, choose Sales form content.
3. Click the pencil icon, then turn off deposit.
4. Click Save.

Please check this article for additional information: Request And Accept Deposits On Estimates in QuickBooks Online.

Also, learn how to categorize transactions once they are downloaded. Go through this article for your guide: Categorize and Match Online Bank Transactions In QuickBooks Online.

Keep me posted if you need anything else about your invoice balance. We're here to help you all the time.