I was getting mold under my wax on cheeses as well , it was getting to be a real problem.
Now I wash them thoroughly in straight vinegar before waxing , I also have been heating my wax up to 250 degrees in a small deep fryer before dipping the cheese , I read somewhere that the high temps kill off most surface flora , between those two changes , I have had no mold under the wax at all on my last 10 or 12 cheeses.
Careful if using deep fryer , as wax can ignite anywhere after 300 degrees or so , I never leave it unattended without unplugging it.
I've had no problems with my white mold cheeses , so can't help much there , but my last batch of red mold cheese (Reblochon) , was getting patches of blue mold all over , I finally scrubbed them down with vinegar and stared a new wash with some new Linens in it , and they have come back the way they should have been , in fact just ate half of one last night and it was great , no hint of the blue was left at all.
I also scrubbed out the cheese cave with vinegar at the same time I vinegar washed the cheeses.
Anyway , that's my experience.