Firefly not seeing some directories

Previously, about 18,000 songs were ripped in a pure Windows environment. Now, I’ve moved the Firefly server to a Linux box so that the server isn’t dependant upon my PC being on.

Here’s the server setup now:
Ubuntu Linux Server 7.10
Firefly Media Server Version svn-1586

The mp3 drive is an external network drive (Ximeta external enclosure). Firefly sees it fine and my soundbridge sees Firefly just fine. The main issue is that when I rip a CD it shows up on the mp3 drive as an unknown file type.

Here’s my ripping setup:
Windows Vista Home Premium
iTunes 7.6.0.29

My wife is ripping with the following setup:
Windows XP
iTunes 7.6.0.29

We can access and play the files after ripping if we use iTunes or if we just navigate to the file on the drive and play it. I’m thinking that this is an issue where iTunes isn’t communicating all of the necessary data (file types, permissions, etc.)

Is there a way to fix this? I’ve tried the usual chmod, chown commands on the affected directories, but I just get the following error: “Input/output error.” If I look at a sub-directory that was ripped, I see this:

drwxrwxrwx 1 root root      0 2008-02-18 09:45 .

drwxrwxrwx 1 root root 258048 2008-02-14 09:49 ..

drwxrwxrwx 1 root root   4096 2007-01-22 08:39 13 Above The Night

?

? ?    ?         ?                ? I See Good Spirits, I See Bad Spirits

Any ideas on how I can:

a. Fix the currently messed up directories/files.
b. Correct the issue with how iTunes rips disc and sends the data to the linux drive.

Thanks for your help!

Johnathan