When creating a profile graph using a 3D line containing sections of no data, the resulting graph will start all sections of the line from left side (0 horizontal distance) of the graph.
There is an enhancement request for this, and I have added the ArcGIS Idea link to it, so if this is a common issue and you want to see it addressed vote for this idea.
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When creating a profile graph using a 3D line containing sections of no data, the resulting graph will start all sections of the line from left side (0 horizontal distance) of the graph.