Yep, taking clones from flowering plants can be tricky. I took a clone of a girl that was 3 weeks in because the plant was developing so nice, and she turned around and was rooted in about 2 weeks and was at 5 nodes a week later ready to be topped. The length of time they are in flower, and the strain can all play a differense in rooting clones from flowering plants.
Keep up the good work partner.
Adieu