If you are having trouble in making the partial payment using WP Travel plugin then here is the thing that you need to be careful of.
Sometime there may be two different pages “WP Travel Dashboard” in the Admin Panel > Pages with the same shortcode in it. If so then then it wont let you complete the payment from the user dashboard using the Partial Payment plugin.
So you need to make sure you have only one WP Travel Dashboard page and correct shortcode
[ wp_travel_user_account ] in it and assign it to the field ” Dashboard Pages” from Admin Panel > WP Travel > Setting > General.