Hello,
I notice that, of the seven pins associated with JP2, none is a ground connection. If JP2 is the only connection with the target, and separate power supplies are used for programmer and target, and these power supplies are isolated, there will be a problem. There must always be a direct ground connection between the programmer and the target.
For a POR to occur, the Vdd voltage must drop below 0.1 volts. It is possible that this does not occur because you have a number of pull-up resistors (to 5V) in the programmer, that are connected pins on the MCU. The current flow into these pins, when Vdd is removed, can cause Vdd to remain above 0.1 volts, and POR will not occur.
The power to the programmer needs to be switched at the same time as the power to the target. Alternatively, you could supply power to the target, via the programmer, and then only the programmer needs to be switched. However, to do it this way will require more than seven connections to the target.
Regards,
Mac