Not that I've ever heard. A lot of people falsely connect the Skull and Bones to Masonry, which isn't true.
The skull and cross bones are the marine battle flag of the Knights Templar. These have been an order of York Rite Masonry for many centuries. Most Knights Templar were burned at the stake by the church for silly reasons in the 14th century. The survivors found refuge in England. The skull and cross bones ravaged catholic shipping for some time thereafter.
Yes the jolly roger is a masonic symbol.
Temperance, Fortitude, Prudence, and Justice.