I use a couple of external eSata drives (Seagate FreeAgent Xtreme). When they start out plugged into the computer, there is never an issue with them showing up in Windows Explorer.
However, if I want to hook them up or move them once the computer is running, I sometimes have issues.
After a little research, I found that while Firewire and USB are fully plug-n-play, eSata is not. This does not mean that you can't hot-swap eSata drives, it just means there is a trick.
It seems that the power to the drive is what triggers it being recognized by Windows. Plug and unplug that eSata cable all you want; it won't do a thing.
However, if you unplug the drive's power cable (I do it at the back of the drive, not the source) and plug it back in (assuming the eSata cable is already plugged in), your drive should appear in Explorer!
Hope this helps.