Also, only microwave the same flowers at the same time, instead of mixing and matching. Cover the stems with silica gel, then place the container and a cup of water to the microwave. The water will absorb most of the energy from the microwave.
Set the microwave to 1-2 minutes, checking every so often with a toothpick to see if the flowers are dry and repeat until dry. Remove and leave them to cool before removing the flowers and stems and dusting them off.
You can use this approach for roses, gerberas, irises, and tulips.