Sit n Donk + HEM

Which part exactly?

Well I am assuming the $EV is calculated wrongly as it might assume that if i had won the hand I would have cashed in the money

i.e. 5 players left, I go allin iwth +EV move and lose. How does it calculate potential tournament earnings?

$EV is calculated wrongly, thats right. You should ignore that - ROI is what you are after. You should probably make some little adjustments and you should be good.

edit: post some hands maybe, 3 and 4-handed mostly, cause that is the single most important part of the STTs.