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This would be a MathType issue. If you are placing your equations as EPS files which is the recommended way with InDesign Mac, the stacking order is already set inside that file; InDesign cannot reorder objects in EPS file.
If the MathType people have no answer for you, the only thing I can suggest is to open these EPS in Illustrator and reposition the strikethrough manually.
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This would be a MathType issue. If you are placing your equations as EPS files which is the recommended way with InDesign Mac, the stacking order is already set inside that file; InDesign cannot reorder objects in EPS file.
If the MathType people have no answer for you, the only thing I can suggest is to open these EPS in Illustrator and reposition the strikethrough manually.
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Thanks for your reply Brad