Invoices not clearing register

I'll help you fix those payments in your bank register, Kahoa.

You may have selected an incorrect account instead of the Undeposited Funds account when recording the payments. 

Usually, the Undeposited Funds account is used to hold payments temporarily. As you proceed to create Deposits, you will find the option to include those payments in the deposit from the said account.

To rectify this issue, when creating payments, ensure to select the Undeposited Funds account. 

If you need to correct existing payments, simply edit them and modify the account to the Undeposited Funds account.

Furthermore, I have attached an article that offers helpful suggestions for troubleshooting common challenges associated with invoice payments: Resolve common issues when applying a payment towards an invoice.

Don't hesitate to comment below if you need additional assistance managing invoice payments and other related issues. I'm always here to help. Have a great day.

My  desktop version doesn’t have the option to select but instead defers to undeposited which is what you suggested I select .  My reconciliations are fine but the uncleared transactions are invoices that have been paid but remain . And my balance in register is effected by the invoices . The invoices are deducted from my balance and never credited back? 
Hoping there is a simple fix to somehow address the invoice issue. I tried deleting them but that gives credit  back to the customer.

@Kahoa 

"The invoices are deducted from my balance and never credited back?"

Invoices should not have any effect on your bank balance.  If the invoice is being deducted from your bank account, then the items on your invoice are mapped to a bank account instead of a revenue account.  Only the payment received on the invoice should increase the bank account selected under the 'Deposit to' drop-down menu.     

Sound like the cause.  If so, when you edit your items you'll see the bank account as the sales account. This is allowed, but not usually right.  If you change the account to an income account, and then save the item, you'll be asked if you want to update your transactions. Answer yes and then the unwanted details will disappear from your bank account register.