Scibility :
IMTECH :
I haven't used MSI's Gaming App, but I've experienced that with other programs. Namely, MSI Afterburner (+RTSS) showing millions of fps in a game. It happens. The solution that worked for me was just to restart the Afterburner.
Not the case for me it does this always so im not sure about my realtime FPS ingames atm, i've had this in windows 7 with gaming app 5 and now in windows 10 gaming app 6 the same issue.
Why don't you try some other software then? If you have an NVIDIA's card, turn on Shadowplay (you don't have to record, just enable it) and set it to show FPS on screen.
Or get
MSI Afterburner - a very popular program that shows you real time FPS, CPU/GPU usage, clock etc.