Do you have lens corrections aberration turned on on your camera (can't remember which camera you are trying to do) but this is known to cause issues, mine was whilst tethered, a message saying "A shot was taken but no focus points reported focus confirmation. You should ensure you are using single point AF mode and that you have an appropriate focus point selected on the camera".
The newer versions of FoCal have a new message suggesting lens corrections as the culprit, but I'm guessing you would only get these messages whilst tethered.
Also, contact Reikan for help, they are great, I got a response in less than a day!
I hope you get to the bottom of this.