The word 'second' has three different meanings and two different pronunciations.
The first meaning is an adjective which means the one after the first. It was imported from Old French (second) by English around 12th century. It was secundus in Latin.
The second meaning is 1/60 of a minute. It was imported from Old French (seconde) by English around 14th century. It was secunda in Latin. Why is it called second? It is short form of secunda pars minuta "second diminished part", named by mathematician Ptolemy.
The third meaning is to support, pronounced as sɪˈkɒnd. It was imported from Middle French (seconder) around 1580, originated from Latin (secundare). Maybe it was imported late and it was very closed to the publishing date of King James Bible when the English pronunciation had been stabilized. The pronunciation of this "second" had not yet localized.