I was having trouble getting KeeOtp to match what Google Authenticator was saying. Additionally when entering the key using the configuration form, it kept getting changed to all 7's when I would later go back to look at the key. After downloading the OTP-Sharp package and comparing what it was showing with Authenticator and looking at the key it was generating, I noticed that it was using an all uppercase key. Out of a whim, I changed my google 2 step key into uppercase and put it in KeeOtp, and this seemed to make everything sync.
If indeed it needs to be all uppercase, the program should change that for you, as Google presents the key in lowercase on their 2-step page.