snapper u gotta remember that stove calculates with 5cards to come so it calcs showdown equity if board is left blank and so on if u enter 3cards in the board panel then it will estimate equity with 2cards to come..The difficult part to calc your ev to see a flop is u have to work out how often an Ace , King or Queen come on the flop for villains AK AQ holdings and then calculating for his bigger pairs QQ+ and a low cooler flop and then factor in your 2 outs to hit to improve turn and river[approx 8%] as long as villain does not improve...The problem is compounded when u factor in at least one opponent happens to hold one of those overcards to your jacks...
u get {50 \choose 3} = 19,600 possible flops so i"ll leave others to work it out
just read through it and i hope u get what i"m trying to explain..
edit - the figures u have from stove estimate the equity for a 5card showdown..