I have found that by reversing the order of pick points for the hatch(es) I have consistently been able to complete the action. I have tried it in both paper space and model space with similar results.
What do you mean by "Toggle through the various scales in your file, then re-hatch." I have a viewport in a particular scale. Do you mean go back to paper space, toggle through, then go back to what the viewport is set at and try again? I tried this and it didn't work.
Or do you mean, while hatching, toggle through the choices of scales, then return to the one that I wanted in the first place, choose that, and hatch? This doesn't work either. The only way I can hatch is to break up big chunks and hatch each separately.