Design a test scene to tank your FPS, then measure it with your own counter.

Use physics to create an ever-growing atomic nucleus.
Use the profiler to investigate performance.
Measure and display the frame rate.
Prevent the creation of temporary strings.
Stabilize the frame rate by averaging multiple frames.
Colorize the frame rate display.

From http://catlikecoding.com/unity/tutorials/frames-per-second/