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Hi there, @Q-BOnlineCustomer.
The automatically apply credits feature should perfectly work fine once it's enabled or disabled from the Accounts and Settings. Just make sure that the correct options are set from the Advanced tab.
- Automatically apply credits for customer transactions.
- Automatically apply bill payments for vendor payments or entries.
Getting strange experiences can be affected by cache which causes unusual behavior while working with QuickBooks. For now, you can follow the workaround provided by LieraMarie_A above to open QuickBooks using a private window. If it works fine, I suggest clearing your browser's cache or using another supported browser to narrow down the result.
If you need help modifying other settings or features in the future, you may also review the resources from this link as your guide: Edit company settings in QuickBooks Online.
If you have any other questions while handling your payment entries in QBO, let me know by adding a comment below. I'm more than happy to help. Keep safe!