With respect to NTFS corrupting, I would say that's a pretty rare occurrence in my experience. It's generally pretty reliable.

But, I would definitely start with a format and I'd probably even consider a full format (just that it will take a while) to completely wipe it.

NTFS corruptions should not cause hard lockups either, so I would suspect hardware issues in turning causing FS issues.

If your eSATA is "unreliable" you really should exclude it from your backup process. You are just adding more risk. It sounds like maybe your backup dock hardware (maybe the power supply) could be the culprit.

Also, 1.5 days for 1800GB is kinda slow too. That's about 14MB/sec. With USB2.0 you should be a bit more like double that.