Seto won three golds in Moscow recently and maintained his high standards when setting a new Asian and World Cup record of 4:00.12 in the 400 IM.
Laszlo Cseh of Hungary came second in 4:01.42 with team-mate David Verraszto third with a time of 4:03.19.
However, Seto was unable to repeat the trick in the 200 fly as he could only finish second behind Nikolay Skvortsov.
The Russian recorded a time of 1:51.77 while Seto was under par with a time of 1:52.22.
In the women's events, Katinka Hosszu suffered a major shock when failing to make the podium in the 200 IM.
The Hungarian had been undefeated at that distance in World Cup events this year but lagged in behind Great Britain's Sophie Allen.