IPod 2nd gen not showing in iTunes

My iPod 2nd gen hadn't been used for a while, and the battery was dead.  I charged it, and connected it to my Mac Mini (1st gen).  It is now continuously blinking orange but is not showing up as a device in iTunes (v. 10.6.3).  According to the manual, the blinking means it's syncing in iTunes, or the iPod shuffle is enabled for disk use.  I don't know what the latter means. 
I'm using the original dock, but it is connected to a USB port on my external hard drive which is connected to the mini, since the 1st gen Mini doesn't have enough USB ports.  (That shouldn't be a problem though, because my 3rd gen iPod nano shows up in iTunes using that same port.) 
I've tried twice to get it to show up in iTunes.  The first time it was already connected to the USB port but wasn't showing any lights, and it didn't show up in iTunes.  I turned the shuffle off, waited 5 seconds, and turned it on again.  Still didn't show up, so I manually removed it from the dock and unplugged the dock. Then I plugged the dock in again, and put the ipod firmly into the dock.  Then the orange blinking lights started, but it didn't show up in iTunes that time either.  I did get an error message that it had not been put away properly.
Since it wasn't showing up anywhere that I could find (iTunes, Finder, Desktop) to eject it, I shut down the computer, removed the iPod from the dock, restarted the computer, opened iTunes and then put the iPod in the dock. It still doesn't show up as a device in the left-side sidebar of iTunes where it usually does, right after Library, Store, and before Playlist).  I can't put it away properly now because I can't find it to eject it. It's still blinking orange.  (The right sidebar only has a message about Genius and learning to use it).
I've read previous questions similar to this, but nothing suggested there has worked.  If anyone has suggestions/idea, it would be greatly appreciated.
My O.S. is 10.5.8.
Thanks,
Esther

Thanks for providing a good amount of detail. 
Enable disk use is a setting (checkbox) on the shuffle's Settings tab in iTunes.  It allows you to see the iPod's "disk" on the Desktop continously while it is connected, so that you can copy files to it using Finder (like it was a USB flash drive).  The light blinks as a warning to eject before disconnecting, because the iPod's disk is mounted.  If that checkbox is NOT checked, iTunes only mounts the iPod's disk when syncing, so the light does not blink most of the time (and you can disconnect it without ejecting).
Although you have confirmed that the USB port on the external drive (Is it an OWC miniStack?), which is the same as a powered USB hub, works with another iPod, you may want to disconnect something from a direct USB port temporarily.  Connect the shuffles docking cable there, to confirm it's not the port causing the problem.
If you connect it and run Disk Utility instead of iTunes, does it appear in the Disk Utility sidebar?
Since this is a 2nd gen shuffle, and you use a Mac, you can try using the iPod Reset Utility
http://support.apple.com/kb/ht1238

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