I'm experiencing a similar issue, but I'm using Evolve software. I've asked to have all cat/O2 systems re-enabled, since they also use a canned tune for catted or catless cars. I'm approximately 200 miles after the flash and still haven't had the cat or O2 sensor flip to READY.
Once your calibration has all systems enabled, you also need to fit your driving into a couple drive cycles:
http://www.europeantransmissions.com...0Procedure.pdf