The "shift" parameter for microtonal scales is incomplete and inadequately explained in the old user interface. It looks like the intent is for it to run from -64 to +63 with 0 for no shift but it really runs from 0 to 63 with 64 as no shift — which means you can't set no shift unless the scale has fewer than 64 notes and you work out an equivalent value
I've got a patch to make the shift editable for its full range. I also made some patches for documenting the parameter and fixing some typos and I'm not sure I can attach all of them, so I'll copy my descriptions of the "shift" here:
Shift the tuning down this number of steps (64 to start on 'A')
Number of steps to shift the scale down by. 64 for no shift.
Here's a patch for some random typos
Patch to add a tooltip
Another documentation patch (I think this is for the file format)
I had another look and got a patch to make it work properly, with zero as zero