Yes, if you stay in the game menu AMD's software is counting the FPS there as well as in game. Like I said, if the card is performing fine in game, who cares what the software claims is "marginal"? You can select "control+alt+o" in game for the overlay that shows the FPS, GPU usage, CPU usage, RAM, VRAM, etc. If all that is ok, you're fine.
"It worked before you broke it!"