Megera wasn't let out, Dodger and another decker broke in to try to get her out, but were too late to stop the reverse engineering and were only able to save her after whe had been corrupted. The Megera personality is what resulted from that, but was still one of only three AI's known to exist on the planet, therefore representing an incredible asset to Renraku. That is why they still wanted an "insane" AI: R&D.
As for Pax, she was the lead Otacu working for Deus. She was NOT implanted with the technology used to keep the other Banded in line and droolingly subservient to Deus. She worked for him because she wanted to. Evil slitch. After the balloon went up on the Arc, she ecaped and pulled together some of the other White Banded (corrupted otacu) that escaped and began forming dissonence pools in the matrix in hopes of strengthening Deus' power when she was able to get him back. Pax knew about the experiments to implant code in thousands of prisoners in teh Arc, and knew how to access then when they were online. Furthermore, she knew how to "reprogram" other Otacu plugged into the matrix, thus the Dissonence Pools. And I seem to remember something about her preventing her own fading by feeding off of other Otacu in some fashion and using Deus' brainwashing techniques to create utter loyalty in her followers.
Gabriel