Without more specifics, I'm not exactly sure where you're looking or what you're seeing. For my part, I haven't noticed any changes in how iFly works in this regard, nor have there been any changes tested in the beta community, so I suspect you're seeing something unique to your usage.
Recall that there are two different places to get "vertical profile"-type information. One is with the instrument that you can add to the moving map screen. The other is from the flight plan, using the "Altitudes" button.
The flight plan method will show the entirety of your flight. It's intended for "strategic" planning--ensuring that the altitudes set in your flight plan are adequate to clear obstacles and terrain across your entire route.
The vertical profile instrument on the moving map is intended for "tactical" planning--it shows a shorter distance, and uses your current altitude and an instantaneous projection of your current rate of climb/descent to help identify near-term obstacle/terrain clearance issues. (It also shows airspace, too.)
Could it be that you're remembering the way the flight plan "altitudes" button presents the info, but looking at the moving map instrument?