Loan updating automatically but payment account is not

Linked loans are problematic in this regard.  Linked loan accounts also do not have a register so you cannot see any transactions nor the allocations of principal, interest, etc.  When your checking account downloads the payment it needs to create and use a standard category (such as "Loan Payment"), not a transfer category so there is no link between the checking account and the loan account.  Because of this most Super Users recommend not linking loans to the lender and instead setting them up as or converting them to manual loans.

Manual loans have registers, let you see the payment schedules and the payment breakdowns between principal and interest.  They also permit you to enter a transfer category from the checking account to the loan without double counting the payment.  And during the manual loan set up process a Reminder will be set up which will enter the monthly payment transactions into both the checking and loan accounts along with all the details for principal, interest, etc.

You might want to read the following to see how to convert loan to a manual loan:  https://community.quicken.com/discussion/7164936/faq-how-do-i-convert-a-loan-account-that-automatically-downloads-transactions-to-a-manual-entry-sc.

Or you can delete your loan account and set up a new one but do not link it to the lender.