KUKA|prc uses some parallelization to calculate with more performance, this is the reason that the order sometimes changes. You could sort the meshes e.g. by the number of vertices - that should not take significant computational power and solve that issue for you.
However, the parallelization happens only internally, to the outside there should not be any special things happening.
I don't know Mindesk, but I could imagine that it generates a mesh and then only updates the position of the vertices when they change. So try the sorting I suggested above first, please.
If that does not help, please let me know if there are any error messages or indicators, what may be going wrong.