Hi John,
When you installed your second drive, did you format it? (To do so, use the eraser icon that appears next to it.)
New drives often come with ntfs on them. Camect will allow you to use a drive like that without formatting, but will warn you when you enable the drive that doing so is subject to data loss and we strongly recommend formatting. If you forcibly use a drive like that anyway, it won't be used automatically when your system restarts, but you can still manually select it to re-enable it. (I'm thinking you have an ntfs drive, and you need to manually select the drive again due to a restart.)
Also, not related to this but worth asking -- If you're using an external drive, be sure to plug it into one of the blue USB 3.0 slots.