Since these are self-consistent loops, there are two factors controlling the simulation time: the time per step and the number of steps. If the number of steps is larger, that easily explains the total time difference - more steps means harder to converge, which can be caused by lots of factors (simply more difficult geometry, more charge transfer, higher bias = more non-linearity in the loop, etc). If the number of steps are similar, and you have longer time / step, then it's either the machine being slower (other processes? more MPI processes per node), or your changes introduced a switch of method - if you have default parameters ATK can sometimes detect a difference that causes it to switch internal methods. Although, in your case I doubt that's the reason, and my money is on more steps, which is easy enough to verify from the log file.