Ah, OK. I thought by your first post that you were losing the default setting to your pictures, or music folders.
So, your selected folders are on an external drive?
Can you give other details -- such as, what kind of connection to your external drive? (connected and powered through a hub, or is the drive self-powered (the drive has its own power supply).
You said that everything seemed OK before Mountain Lion... What version of macOS are you using now (and which model Mac?)