If you ever got a windows blue screen issue after activating the configuration on TwinCAT and clicking OK to "Restart TwinCAT System in Run Mode", you can follow the steps to fix this problem:

1. Go to your TwinCAT boot folder: "C:\TwinCAT\3.1\Boot" and delete the content
2. Restart your IPC
3. While in config mode + free run toggled on, Once you have all the adapters correctly selected, hit Reload Devices button.
4. Check the EtherCAT Master’s -> Online tab to verify all of the IO is in OP mode.
5. Assuming no error pops up from hitting the Reload Devices button, move onto disabling the Autostart boot project setting for the PLC project.
6. Activate configuration and click OK to "Restart TwinCAT System in Run Mode".
7. If you do not see the blue screen, it is fixed! 
8. Upon logging into the PLC, if you see the blue screen or things lock up on you and you need to reboot, then the issue is coming from the PLC code. Something in the code is triggering an exception (divide by zero, null pointer, array out of bounds).
9. You can alter or isolate breakpoints around to figure out where exactly the code is hitting an exception.
10. When you fix the issue in your PLC logic and the program is free of errors, you can try activating again.  

It is a good practice unchecking the Autostart Boot Project setting for the PLC project until you are sure that your program is free of errors.