I had a doubt on the solution because the D3 pin is not used and must stay low. But WxPic has not been designed to drive an unused pin. The solution I used with the configuration file is to let the pin in its default state. I expected that this would be Low.
As your test failed, I dig in the software and I found that the default value is 1 for unused pins.
I cannot propose you to drive Low the D3 pin when the programming starts because this would mean that at the end of programming the D3 pin would be brought back high with the risk to burn the device.
So as a quick workaround, I made for you a
modified WxPic executable that drives unused pins low by default. You must decompress the executable and place it in the WxPic installation directory to replace the old binary. You must still use the configuration file attached to the above post.
I hope that I can do a better fix later in a future version. Nevertheless this programmer stays very risky because it might apply VPP on wrong pin if there is a problem with the software. It would have been better to use a hardware switch to route the VPP to the right pin rather than relying on the programming software.