Mike, that's almost certainly why you're having problems. Beeswax is like any other oil, it will contaminate a mold cavity preventing bullet fill-out. The hot boiling water should remove it. Here's a link to a place that sells a lube that just plain works for lubing molds;
http://bullshop.gunloads.com/tbs_lube.htm
Order some bull plate sprue lube. It's a high temp silicone type lube that prevents galling of the top of any mold. It also is great for guide pins and the handle pivots. Be prepared for a long wait for delivery. Dan lives in a remote area of Alaska, he only goes into town twice a month and to his mailbox,(which is 7 miles from his house), every couple of days.
You use a verrrrrry light coating of it under the sprue plate to prevent lead smears on top of the mold and under the sprue plate.