We also use vermiculite and have never had a problem with it. If you are using a covered egg box drill a few small holes in the top to control excess humidity and be sure it is not overly damp to start with.Generally we let all our females follow through on their natural laying ritual, let them burry their eggs (to their satisfaction
, remove them and then dig out the eggs. I'm sure you have seen dragons burying and know that they are fairly rough with the eggs. As long as you get to them fairly soon after laying, you need not worry about placing them in the incubation medium in any particular way.
Sometimes there are losses for no particular reason but if they are excessive it may be attributed to husbandry.