Quote from WingsOfLife
Though this isn't quite the place for bukkit modding, it appears your armed variable is global therefore causing all chests in the world to become armed and unarmed. (Im no bukkit modder though.)
Yea I actually made some other adjustments right now so that the each unique chest is an index in an ArrayList as well as a seperate ArrayList to keep track of a counter for the matching index so that when the number is odd it will arm the bomb and when it is even it will disarm it. I just don't know what I am doing wrong.