put a voltmeter to the yellow and red with the car turned off and on
Yellow should always show +12v regardless
Red should only show +12v when in the ACC or ON position
Did you say whether or not the clock reset if you just left the car in ON or ACC without trying to start it?
Someone else also suggested to use a voltmeter to test out the voltage. I haven't gotten around to getting one yet, but at first glance, I'd like to assume I'm getting the correct power feeds since my clock retains the time setting if I go from a OFF to ACC, OFF to ON.
I did a bit more investigating last night, and here's what I found:
For starters, my car is a manual transmission, so I need to push on the clutch before starting the car in order to fire it up.
Key positions are:
1.) Off
2.) ACC
3.) On
4.) Crank (which will spring back to On after released)
Basically I was only able to replicate the problem if I put the key in either ACC or On for 4-5 seconds, and crank the motor. The unit will reboot while the engine is cranking and time settings will be lost.
I tried doing the same exact thing without cranking the motor (put the key in crank position without the clutch in), and the unit did NOT lose the time settings.
If I crank the car straight from Off, the unit will only boot once, and the time setting will retain.
So it seems that something in the unit doesn't like it when the unit has to bootup twice in such a short amount of time while the engine is cranking.
But, luckily there's an auto-correction feature on the unit, so if all else fails, I can always fall back on that. 
I'm not sure if it matters either, but I performed the software bypass on the unit as well. So my e-brake wire is grounded, and the parking_brake_speed value is set to 128.0. My data.zip file is derived from the 2.0 update folder on the Pioneer site.
And I know I forgot to mention it, but the unit did come with the 2.0 firmware update.