Hello Stephen,
A bit hidden in the old user guide, the desorption distributions are explained on page 25. The reflection types (p27) are the same - diffuse corresponds to cosine and uniform means all angles have equal probability.
Your MATLAB code and Molflow should get exactly the same results, my guess would be that you're comparing the Molflow pressure to your MATLAB code's number of hits. As pressure depends on the incident angle, for such comparisons you most likely need the impingement rate (you can choose it in the texture plotter's dropdown menu) or the raw number of Monte Carlo hits.
If that's not the case, send me your MATLAB results with a brief explanation of how they are generated, and I'll have a look!
One last thing: the old user guide, written in 2013 isn't updated anymore, so if you're interested what Molflow is doing under the hood, you can have a look at section 1.2 of my thesis.