The Fibonacci sequence is periodic modulo every positive integer $m>1$, and perhaps more surprisingly, each period has exactly 1, 2, or 4 zeros that are evenly spaced, which also holds true for more general $K$-Fibonacci sequences. This paper proves several conjectures connecting the zeros in the Pisano period to the prime factors of $K$-Fibonacci numbers. The congruence classes of indices for $K$-Fibonacci numbers that are multiples of the prime factors of $m$ completely determine the number of zeroes in the Pisano period modulo $m$.