Why is it beneficial to have a diode in series with a VPP resistor?
Normally a Vpp has other duties when not being used for programming, such as RST. Typical wiring is a resistor and diode in series to a 5 volt source, and a connection through a resistor to a normally OFF 12 volt source. When the Vpp pin senses 12 volts in puts the IC into program mode.

The diode is to prevent 12 volts from feeding back into the 5 volt line, which normally has a 10K ohm or so pull up resistor to 5 volts to reset the IC.

I suspect your IC is being damaged by having the 12 volts ON all the time, acting also as a pull up for the RST pin. Under normal operation it is connected to ground through a 10K resistor.

The 12 volts should be turned OFF the moment programming is done.