The pair are now seventh in the 15-boat fleet and are still feeling the effects of being loaded with a 50 per cent penalty on their first-day results after their boat was deemed to be underweight when measured before the regatta started.
That saw Maloney and Meech 13th after the first day's racing.
It was a challenging day for fellow Kiwis Josh Porebski and Trent Rippey, who carded two 13ths and a ninth in the 16-boat 49er fleet to slip one place in the overall standings to eighth. The pair had visions of a top-three finish in Santander and will need to sail well in the second half of the regatta to get back in touch.
There are two more days of racing for the skiff fleets before the double-points medal race.
The World Cup final is Maloney and Meech's first major regatta since winning silver at the Rio Olympics. The conditions have proved challenging at the invitational event, and today saw an 11- to 16-knot breeze, gusting to 25 knots.
"Points-wise, it wasn't the best day but we were sailing pretty well and had some good things to take away from the day," Maloney said.
"We kept fighting in each race and climbed our way back up the fleet. Our speed was pretty good and we did a lot right on the course. Our objectives tomorrow are to practice getting off the line and keeping it simple on the upwind legs. And to also have a really solid and fun day out on the water."