Yes, the defaulting of the scratch disk to the main OS drive can cause lots of problems. I've traced dropped frames, sync problems etc. to the scratch being the main drive.

Sony makes a tape backup solution that will backup your project files and the raw footage. I've seen it advertised in various sources but don't know much about it. What always struck me as a little odd is that the product was specifically designed for Macs - it isn't available for PCs.