Thanks Mike, all is working fine now

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The Data Sheet B0261 for the ATOM Pro 64 TQFP needs revision to reflect this...BM take note.
The Data sheet shows the A/D ports under the label P0 to P3 and P28 to P31. These do not work for A/D. The data sheet also correctly shows the A/D ports under P40 to P47 which work fine.
The ATOM Pro 40 connects some ports together to meet the limit of only 40 physical pins on the module. The Pro 64 has no such limitations so there is no need to connect any ports together. My guess is that the Pro 64 data sheet was an edited version of the Pro 40 data sheet and that the author didnt make the appropriate changes to "disconnect" (separate) the connected pins! So functions other than A/D may also be shown incorrectly for P0 to P31.
Be carefull with the description of ports P0 to P31 on the data sheet. Some of the functionality shown for these ports is, in fact, only available on ports P34 to P52 on the Pro 64. P34 to P52 are the ports that are connected to other ports on the Pro 40 to fit within the modules physical limitation of only 40 pins.
For what its worth, my concerns with the programming protocol were unfounded, the circuitry associated with the RESET pin is not critical and, in fact, the chip will program without the "critical" diode in circuit! A simple RC pullup on RESET appears to be all that is required.
Again thanks,
Peter Strong