Okay, this has bothered me for awhile, so here goes...
It was established back in the Pilot episode that Professor Farnsworth is Frye's nephew, removed by a couple dozen generations. Presumably this means that Hubert is a descendant of Frye's brother Yancey, possibly (but not definitely) through Yancey's son Phillip. (Although this wouldn't explain why the Professor apparently didn't know his ancestor was the first man on Mars.)
HOWEVER...in the Roswell episode a time paradox occurs that makes Frye his own Grandfather. Which would mean Yancey is also his grandson, and any of Yancey's descendants would also be DIRECT descendants of Frye.
SO...Professor Farnsworth would have to be Frye's great-great-however many times-great GRANDSON, not nephew...right? Although I guess, technically, Frye is BOTH his grandfather and uncle. Strange, but true!
Gary