Process mining with ML
I suspect that the problem has more to do with your data than with your algorithms. My recommendation is to spend some time studying your data and ensuring that it is a robust representation of the kinds of problems you're expecting to solve. If possible, come up with a way to generate extra data. Given the fact that you already have many permutations, you could perhaps write a script to create additional permutations by modifying existing samples with rules that you know.