@Ann.TRT, check your start date under Starting Balances in Settings. If that accidentally was set to some date in the future, your receipts against past sales invoices would be ignored until that date arrives. See https://www.manager.io/guides/9783.
If the start date is not your problem, post a screen shot of the Edit screen for one of these receipts that should have been applied to a sales invoice but was not.
@sharpdrivetek was referring to specific designation of the sales invoice rather than just the customer. If, by “auto received” you are referring to clicking the New Receipt button while viewing the invoice involved, Manager is automatically making that selection for you. This process is only truly manual if you create the receipt from scratch.