There is no reason for eSATA to be any less reliable than the onboard SATA ports: eSATA == SATA, 100% except for the connector.

So perhaps that's a good place to focus attention. Exactly how does the external drive connect to the motherboard when using SATA ? What is the path of physical cables (and lengths) that is used?

As for diagnosing the drive, YOU REALLY MUST GET THE S.M.A.R.T. DATA!! Pardon the emphasis, but that is the first and FIRST step required.

If you cannot get it under MS-Windows, then boot from a Linux disc and get it from a terminal window with "smartctl -a /dev/sda".

Cheers