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.
I've come across this issue before, just assumed it was a bug?
My guess is that the profile graph is intended to display/use M and Z but disregard X/Y.
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.
Retrieving data ...