Tell me one thing... what is "the other program", and what value does it give you for the conductance 3-->1?
Let me know, please.
Anyway, I just noticed that in your new file you generate molecules on facet 1, so you're calculating the conductance to 1-->3. Also, your formula is not correct, it reads...
A3/D1*11.77*AR3
... while it should be A3/D1*11.77*AR1 ... the area is the area of the desorbing facet, in your case no.1.
For the 3-->1 conductance case, as per your description above, the formula should be changed to
A1/D3*11.77*AR3
... after you remove desorption from facet 1 and set it to facet 3.