You're mixing up two completely different things.

In Syndrome X, the "X" just means unknown. For the longest time, the medical community understood there was a syndrome, but lacked the knowledge to understand why. That knowledge is slowly increasing and so that's why we have terms like PCOS and insulin resistance, and everything else that falls in line with it. It's like the X just represented this large unknown. Kind of like why Malcolm X has X in his name, or why Generation X was named X.

In genetic disorders such as Downs Syndrom, it's an "x" disorder because the anomoly occurs on the X chromosome. Other genetic disorders are "y" disorders because they occur on the Y chromosome and thus affect only men.