I only had one disk attached at a time, when I uploaded car2.builder, ran through that, and THEN uploaded 1.03 ( again with just one disk attached at a time ). You just then need to add a jumper to whichever HD will be SLAVE.

Sounds like you know what you are doing so maybe you have already tried this ?

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Rod ,UK Mk2a Sn:1911 Mk2 64gig S/No:341
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Rod, UK