Hey, I'm really sorry to hear that!
The game might not be registering your active focus on that window.
What OS are you running? Could you try running in windowed mode first by pressing ALT+Enter after opening the executable?
I'd appreciate an image or more details about the problem. If possible, send me an email at waifuboxdev@gmail.com.
Thanks a lot and sorry again for the trouble! I look forward to fixing this together.