I am experiencing the same thing I have noticed that before I run the PS3 set up
that if I run /etc/init.d/bluetooth status The bluetooth is up and running but after the PS3 install if I run /etc/init.d/bluetooth status it shows failed even with a reboot
than if I uninstall the PS3 controller Bluetooth is up and running when I run /etc/init.d/bluetooth status
Note I have experienced this with retropie 3.2 and 3.2.1
I also test this with a CSR 4.0 BT Dongle and A Plugable BT 4.0 dongle
I am cross posting since the Bluetooth issue might be separate