The problem isn't that it is "losing" the source.
When a USB drive is plugged in it has to be initialized by the OS, in this case the myLink, and read. While on a computer this is normal and expected, the myLink system seems to have been set with a timeout that is under the threshold for a thumb drive. So when you initially start the car up with the drive in, the system takes more time to initialize and index it than the programmers thought it would need.
Simple fix GM: Software update that increases the timeout before switching sources due to "No USB Drive Found."