After enabling partial payment it is set to 10% by default. (I am using PayPal)
I changed the value to 30% and saved it. When I went to test the booking it is only calculating 10% which was the default rather than 30% which I set.
On Disabling this option, the partial payment percentage is set from the individual trip which is by default 10%. When you enable the global option, the partial payment % is set from the % set in Admin Panel > WP Travel > Settings > Payment > Partial Payment