Wow - I found myself having the same problem again! This time in 10.3.1. I thought it was a source data issue until I used the Identify tool to examine the cell values and found that they are floating point values. Without any particularly compelling solutions to this issue in the forum, but I tried changing the projection as someone else had, and it resolved the issue here. For whatever reason, simply switching the coordinate system for the map document from UTM NAD 83 to UTM WGS 84 allow the Interpolate Line --> Profile Graph function to output a graph with floating point values on the y-axis.
Anyone know why this is happening?
It looks like this is a known bug:
NIM063478: 3D Analyst Toolbar Interpolate Line tool rounds z values.