Some people are having difficulties to achieve consistent results compared to WUFI1D.
To set up a one dimensional case in WUFI2D assign adiabatic transfer coefficients at two sides (e.g. left and right) to your construction.
You can use a very coarse grid in this direction to reduce time of calculation (You could even edit the input file and the program will be faster than WUFI1D - somewhen I'll post an example how to do that).
Refine the convergence criterion (numerical settings -> advanced) to something like 5E-6 and perhaps the maximum number of iterations (maxit) to sth. like 500 (In WUFI1D this parameter is min(200,4*ni) with ni=total number of elements).
Be aware that the Heat Transfer Coefficient in WUFI2D is in W/(m^2 K) and in WUFI1D the inverse of the HTC called Heat Resistance is in (m^2 K)/W.