Lastest Update 10.4.3 & External Hard Drive Problems?

My problems started 2 days ago when I could not copy new music to my ipod shuffle. I kept getting error "...could not be read from or written to..." I had run the new ipod update 1.1.3 so I restored to factory settings and used previous updater 1.1.2. Seemed to be fine for the time being. Later I tried to import music from a CD, wouldn't import, same message. Tried to download a song from the Music Store, same thing.
(For some additional info, I have 2 external hard drives. On hard drive One I keep my iTunes media, iPhoto media and a mirror backup of my Documents folder from my internal drive, and miscellaneous other big files I don't want to bog down my internal drive. My second external hard drive is just for digital media when running final cut pro. I dont' use this drive much. The first hard drive is not partitioned but the second one is and I noticed yesterday that only one partition was coming up.
I began to realize that my problem with iTunes was not with iTunes itself but a drive issue. I did a quick test and set the internal drive as the main drive to store iTunes music to and did a test download from the Music Store and it worked just fine. So now my problem is something related to perhaps the latest update to 10.4.3 and my external drives.
Just a couple things I tried this morning before I had to leave for work.
1)Tried to copy a file to the external drive one and it wouldn't copy. Got a message saying the file name was too long, which no matter how short I make the name, nothing will copy to the drive.
2) Tried to open a photo from the external drive in Photoshop and it wouldn't open.
3) Strangley, I can still just play music in iTunes even though coming off the same drive as the above issue #2.
4) General question. When I do updates is it wise to not have external drives turned on when updating. I remembered that I did have them turned on when I did lastest update.
Perhaps this is my error.
Anyone else having external hard drive issues, please send your ideas my way...
thanks

I did install the combo update 10.4.3 again and it helped one of my drives. Luckily it's the one I use everyday with my iTunes, and iPhoto libraries and all my other important stuff. The second drive that's partitioned into 3 parts still had problems. One more partition came back bur the third part I just couldn't retrieve and had to blank it. I also had an issue with a corrupt iphoto library and had to rebuild my library.
So I'm almost back up to having my problems resolved. I have also noticed speed issues. Things seem a bit slower since the update. I'll keep workin on it.

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