With the Checkout-plugin enabled please try this:
1. Go to Settings > WooCommerce Extended Coupon Features
2. Enable ‘Debug mode’ and click ‘Save changes’
3. Disable ‘autocoupon’ and click ‘Save changes’
4. Please test if the problem at checkout persists
5. Enable ‘autocoupon’, disable ‘Debug mode’ and click ‘Save changes’
Please let me know the result of step 4.