Going through a considerable trek-a-thon, I have been giving thought to THEWeirdo's continuity error in the Borg storyline.
Hai-Etlik's hypothesis could be true, however it has a strong smack of conspiracy theory to it.
Captain Janeway however has just given me the answer.
Seven of Nine's parents thought of themselves as explorers but had nothing to do with the Federation. In an effort to find somewhere to explore they pointed their ship in the direction of the delta quadrant. They were not searching for the Borg, and they were not heard from again. When Chakotay connected to Sevens neural link he discovered her real name. On reviewing her file Janeway discovered this history and concluded that Sevens family was assimilated by the Borg. This is later confirmed by Seven when she reveals that she watched her parents assimilated. This happened prior to the Enterprise's first encounter with the Borg, but the Federation was unaware as her parents were not affiliated with them.
Where better to look for Star Trek history than in Star Trek itself.
Reference: Star Trek: Voyager - Season 4, Episode 2 - The Gift