Cheat engine
I think you're going about the detection of this the wrong way;
The cheat engine speeds up time for the game; looking at BGE's demo of it, the game clock was running faster.
So don't time the runs, have the client send pings to the server. Do it once a minute. If they arrive every 15/30 seconds rather than every minute you know you have someone cheating. Internet connection quality will affect the pings coming through, but it'll make the gaps between two pings semi-random; it's not going to make 20 pins turn up in 10 mins unless someone is cheating.
This is called a heartbeat and it's common in commercial apps to check that vital servers are running. You probably have something similar to alert your tech support team if your server crashes.
