So, I hope I understand the definitions correctly. Here's a way to construct an example with $k = 3$ genders (say A, B and C) using $n = 9$ sex chromosomes, which I will take to be the elements of $\mathbb{Z}/9\mathbb{Z}$: start with all 165 multisets of chromosomes unused. Choose any unused multiset $\{x, y, z\}$, and add it, together with the multisets $\{x + 3, y + 3, z + 3\}$ and $\{x + 6, y + 6, z + 6\}$, to gender A, add the multisets $\{x + 1, y + 1, z + 1\}, \{x + 4, y + 4, z + 4\}, \{x + 7, y + 7, z + 7\}$ to gender B and add the multisets $\{x + 2, y + 2, z + 2\}, \{x + 5, y + 5, z + 5\}, \{x + 8, y + 8, z + 8\}$ to gender C. Continue until every multiset of chromosomes is used up. The resulting genders (each consisting of 55 multisets of chromosomes) are totally symmetric and so (if I'm not mistaken) are balanced.
It's easy to see how to construct a wide variety of similar gender partitions for given $k$ if we may choose $n$ appropriately. These partitions have nice symmetry and use all possible multisets of chromosomes. This says nothing at all about, say, constructing gender partitions for $n = 2$ (though I believe that I've confirmed by case analysis that there are no balanced gender partitions for $k = 3$ and $n = 2$).
