When you profile using the profile/merge tool the track remains highlighted (default = pink) so yes, you cannot see any shading. If you right click in the map window the highlight will go away.
Alternatively, don't use the profile/merge tool, just stay in "pan" (hand) mode, and right click on the track you wish to be profile and select "profile." The track will stay highlighted when the right click menu is open, but it will go away after you select profile.