To the first problem with loss of tail control when the battery is almost dead - This is actually the case with all of the micros that I've flown that utilize a separate motor for the tail as opposed to having a driven tail. The bad news is that since the Piccoboard pro utilizes a HH gyro (instead of a rate gyro as in the H-Bird, etc.), you don't realize that the mixer is overcompensating for lack of tail control until it's too late. With a rate gyro on a Microelectric heli, you notice the tail start to drift as the battery depletes itself and you have to gradually apply more and more right rudder or right rudder trim to compensate. With the HH, there's not much you can do when there's not enough power left to maintain tail.
No worries, though - There are actually 2 great ways the Piccolo will let you know that the flight battery is near the end of its flight.
1 - You will notice the headspeed gradually decreasing as you induce more drag by increasing the collective to maintain altitude. At some point, you should actually notice that in order to maintain hover you're manually comensating for the decrease in power by increasing throttle/ collective. For example- If you normally hover at half stick on a fresh pack and you're holding 2/3-3/4 stick, it's time to land.
2 - The other way you can tell (my favorite) is watch what the heli is doing. The Piccolo Pro, and other electric collective-pitch helis I've flown have a tendency to "head-bob" or "gyrate" when nearing the end of the flight battery- This is likely due to the decrease in headspeed. Good to watch for it; it's actually kind of cute
Don't mess with your ATV settings to resolve this problem. With a HH gyro the ATV settings will only tell your gyro how quickly to make a singe revolution- The higher the ATV setting the faster your tail will appear to respond to rudder stick input - You would think that increasing the rudder ATV will give you more tail authority, but it's a bit of a double edged sword on an electric motor-driven tail. At a high ATV setting and with a low battery, your gyro will "give up" sooner since it has less available power to make the correction that you're asking for at the speed you're asking it to do it in.
You may try adjusting the mixer on the board instead - I have mine adjusted so that as I begin to spool up the main rotor, the tail motor is running at very high speed - This will force the helicopter (still on the ground) to yaw to the right - As soon as it does, the gyro will sense the tail movement that just occured with no rudder stick input and immediately correct - This actually works the same as revo-mixing in your transmitter - Works pretty well.
Sorry I can't help you on the intermittent tracking problem.
Good luck, and enjoy your piccolo.