When you start up your PS3, delete all of the targets you have saved in ProDG Target Manager. Now search for your PS3's IP. Once it has found it, set it as a Debugging Station then select Add Target, then try connecting from ProDG Target Manager to your PS3.
I've had similar problems where it can connect in ProDG Target Manager but I cannot connect and attach in tools via TMAPI. I've found that doing this step resolves the issue for me so it might help you out.