from The Century Dictionary and Cyclopedia
- n. A flag hoisted at the jack-staff.
Sorry, no etymologies found.
And if the admiral make a weft with his jack-flag upon the flagstaff on the mizen topmast-head and fire a gun, then the outwardmost ship on the larboard side is to clap upon a wind with his larboard tacks aboard, and all the squadrons as they have ranked themselves are presently to clap upon a wind and stand after him in a line.
Dictionary_ inclines to the simple explanation that 'jack' was used in this case in its common diminutive sense, and that 'jack-flag' was merely a small flag.