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The position of the alignment marks were fine, as is the software, but the data wasn't. The encoders weren't storing a correct set up value on both axes for the alignment position - meaning:
1) On alignment each star looked like it was 90 degrees out of position and
2) Each motor was almost guarannteed to knock into each other on half of all gotos
So in alignment position I assummed each axis should read 0 00 00 or 90 00 00, but one on 90 and one on zero seemed confused.
What did surprise me last night when I finished up and went into hibernation I read the axes and they said 90 and 90, even though I'd adjusted them to be 0 and 0 on set-up.
So once the weather clears I will try them again.
Oh and I fixed up a really annoying DEC backlash - somehow the settings had moved from 0 to 18, setting it back to 0 fixed everything.
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