I find to get the best results from embedding wire into foundation, the "frame board" or "foundation board" has to be of the correct height. If the support board for the foundation is too low then the wires are getting pushed down or bowed down in the middle and the ends of the wire will not be embedded into the wax foundation. With the wired frame inserted into the frame board the wires should be laying on the support board.
Also like to run a small fan blowing on the frame while using the embedder. The transformer I use take a "5" count to heat up enough, let off of the switch and hold in place until the wax solidifies, This is where the small fan comes into play, it cools the wax just a tad faster.
Also on the outer pins, I took a small file and cut a small shallow groove into the end pins, this will let the wire fall into the groove and stay in place a little better.