What version of the tool are you on?
Can you try updating to the latest available version to see if the issue persists?
If you continue to experience your issue can you let it run at the point it gets stuck for a couple minutes and then send us the log file located here.
C:\\Users\\<username>\\AppData\\Local\\Red Gate\\Logs\\SQL Source Control 3
You can email the log file to firstname.lastname@example.org
Please include your supprt reference number F0070484 in the subject header.