1) This is due to a conflict with the FTDI chip when the USB cable is plugged in. It is not an issue in the field, when the board is powered the normal way, with the ESC.
2) If this troubles you, we will be releasing instructions on how to modify the board (cutting a trace and soldering a wire jumper) to avoid it. The next batch of boards will have this fixed.
3) Needless to say, if your IMU shield is on the bottom and you're using the reset button on the APM board, there is no problem.
4) Remember that when you upload code to APM, Arduino automatically resets the board, so no manual reset is required. So you shouldn't have to use this button in normal operations anyway.