We had a sub domain website (very small... four or five pages) that was blocked via the robots.txt file for two or three years. When we decided to have it indexed I did just what you did; fetch via GWT and clicked the button to add it to the index. This worked and then the next day... or maybe two days later, it was gone. I did this a couple of times...
It didn't hit the index and stick for two weeks. But since then everything has been just fine.