I can't comment on any problems with earning miles with Enrich when you fly partner airlines but my experience is that I've never really had a problem having miles credited to my account when I fly with Malaysian, if I've quoted the number in my reservation and ensure that my number is in the system on check-in. Miles don't seem to appear when one of the 2 has not been done. I have found the Enrich website to be very helpful in crediting missing miles. They don't always acknowledge that you've made a claim but the miles suddenly appear after a few weeks from submitting the boarding passes.
What I do find very strange is that I can't put in my Enrich number when I fly on Air France or make a booking with them. Do you have to submit the boarding passes to the Enrich claims department every time you fly on an Air France flight??