So far after checking the circuit I have replaced several capacitors and have some limited success. I now have it working completely using an older 286 pc with the software timing loop version of the software.

However on the same machine the hardware timing loop version still doesn't work. From this I can only assume that either the 5v supply is dropping at the start of programming cycle or the 12v/5v lm317 is cannot jump betweem the levels fast enough.

One thing, I did have to make a minor substitution for the 5v reg, I am using a 78S05, with a 20Vdc supply for power.