Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.
Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong, myself and invited authors from the Points of View series.
When overlapping zoom regions are defined, the zoom level at an ideogram position is taken to be the highest (in absolute terms) zoom of any overlapping regions.
For example, if you define the following regions
100-200Mb - 2x 150-180Mb - 3x 160-170Mb - 5x
then the net effect will be as if you defined
100-150Mb - 2x 150-160Mb - 3x 160-170Mb - 5x 170-180Mb - 3x 180-200Mb - 2x
The zoom precedence is defined by the absolute zoom level, which is taken to be max(scale,1/scale) For example, a scale of 0.1 (absolute zoom = 1/0.1 = 10x) overrides any zoom setting with an absolute zoom level smaller than 10x.