Very interesting problem there.

Yes, I see how you would want to preserve the tag info after downloading, and yes, Jemplode is the way to do that, so I see your dilemma.

Quote:
I'm thinking mabye the problem files are on the second drive and jEmplode can't see them?

That's an interesting theory, and it would be nice to know if that's the case for sure. You can find out by identifying problem FIDs and poking around with FTP.

Here's something worth trying:

In Jemplode options there is a checkbox "Use Hijack when Possible." Try toggling that (whatever it's set to now, set it to its opposite) and see if that solves the problem.

Report back.