I see that Bruce had added a link from his site to the online Newgate Calendar, where details are given of the life and death of the highwayman Patrick Flemming:

PATRICK FLEMMING. An Irish Highwayman who held Sway near the Bog of Allen and, after numerous Murders, was executed On 24th of April, 1650

It appears that Whisky in the Jar, or whatever you prefer to call it, was a stage song based on the earlier broadside Patrick Flemming or Flemmen; the powder-dampening episode being retained while other details were changed. Although it's possible that the chorus may have some meaning on the lines of some the ingenious suggestions made earlier in this thread, it's probably just as likely that it's meaningless "cod Irish" of the music-hall variety.