In the first chapter, when the boys meet for the first time, there are several things that suggest reasons for why the boys will not vote for Jack and instead vote for Ralph. The first is an element of uncertainty connected to Jack and the choir's entrance to the meeting that perhaps made some of the boys not trust Jack. Even though they saw him command the attention of the choir, they also saw that the some members of the choir seemed hesitant to obey or unhappy with his leadership. This may play a role in them voting for Ralph instead.
There is also apparently an air of leadership about Ralph, something special about him that Jack simply doesn't have. Golding writes that "there was a stillness about Ralph as he sat that marked him out: there was his size, and attractive appearance; and most obscurely, yet most powerfully, there was the conch."
And the final phrase there may be the key. Along with the "stillness... that marked him out," the conch has quickly become a symbol of authority as soon as Ralph figured out how to blow it. This may very well have been the factor that led to him getting the most votes despite Jack being an obvious leader.