It could have been the screend bottom board not allowing the queen pharamone to permiate the hive good, or it could have been too much room for them in the double medium right off the bat. A colony will abscond for many reasons, I find that the most reliable method to use is once the bees are in the box, throw a queen excluder under the hive body and above the bottom board. They won't leave without the queen and she can't get out at that point.