After about 27.3 GB (the size of my functioning 30 GB drive) it locked up. (...) So, I conclude that the second drive is still not working right.

Just because it died after 30 gigs doesn't necessarily mean it was the second drive's fault. As stated here, some of the songs probably went onto the second drive just fine.

It could have been a heat-related thing. The player might have just gotten too hot with both drives spinning for 12 hours straight nonstop-- its normal operating mode has the drives spun down for most of the time and I could easily see it getting too hot after 12 hours, even if it's sitting in the open air on a desk. Perhaps doing your music uploads in smaller batches is the key.

Also, it could have been any number of other errors, such as a Windows error that has no relation to the player. You said "it locked up" but you didn't define it.