Middle names in
France are usually given after ancestors and family members, and it's not unusual to find the occasional female family name given to a male child. So
Eleonore may have been your ancestor's grandmother, or aunt, or cousin.
For example:
http://www.behindthename.com/bb/baby/4524926 - this is a list of recent birth announcements; amongst the male names you'll find a boy with the middle name
Isabelle.