Weird! The amixer setting 'sticks' on my system; not sure why yours resets. But anyway...you could add the amixer command in /etc/rc.local (the 'sudo' part isn't needed there) to make it run each time.
Regarding scrolling speed, there's a line near the top of PiPhi.py:
- Code: Select all | TOGGLE FULL SIZE
MAX_FPS = 6 if RGB_LCD else 4
That's frames per second. The color LCDs refresh quicker, hence the different values there.
As for color, search for 'backlight' in the code to locate those lines where the color is being set. Legit values are:
lcd.ON (same as lcd.WHITE)