I am experiencing the same issue and thinking not to use Intuit to collect customers payments anymore. It is very ridiculous that partial payment will automatically mark the invoice as closed or fully paid. It causes confusion to customers, inconvenience to business owners as well as providing a chance for business owner to switch Intuit to other third party agency, such as Paypal. Intuit is a big company and this should be a very minor issue to your Tech team. Just do not understand why it is still an issue nowadays.