I have exactly the same problem as the original Author ! I have an AVIC Z3 with 2012 map update (so I assume that I have the latest firmware too).
The unit was working perfectly fine, when suddenly one day, it started to act strange and gets stuck at the "starting up pioneer car navigation..." screen. After 2 to 3 minutes, the Pioneer logo appears and from that point of time, it takes around 30 seconds to boot. Once booted, the unit operates normally !!
I have tried most usual suspects - Method 1 reset, method 2 reset, method 3 reset (lost all my music and personal settings) - made no