My music on iTunes has gone completely wrong. Could anyone please help me?

Question

Hello everyone. I'll try and keep this as unconvoluted as possible so here goes...
I have iTunes 10.4.1.10, although the problem started with the previous update. I was trying to sync music from a Top rated playlist to a new iPhone (a 3GS with up-to-date-software) when I noticed that some of the albums which I had previously has on had disappeared. All of  my albums are saved onto an external hard drive, but the album icons were not on the music library. I put the albums back on (and a few new ones) and a message came up saying that the albums/songs were already there and would I like to replace them; I clicked the 'yes' button. I went about giving the songs I wanted in my Top Rated with no problems and went to sync them as normal. This is where it goes wrong.
iTunes goes through the syncing motions (Steps 1 and 2), reaches Step 3 where it syncs the songs, syncs about 40 of the songs (there are 770 in total) before reaching one of the songs which I had found missing and had put on again. iTunes crashes ( I think that describes it: the 'syncing bar' at the top stays frozen on the song, it will not shut down but everntually stops trying to syns and I can shut it down again; and when I look at the iPod on my iPhone it says cancelling sync and then that it is updating the library before going back to normal).
This was done on the first attempts, now when I try it syncs one songs before the problem song before going wrong. A thing to note about the song before is that the song that ends up on my ipod isn't the one it said that it was syncing, and the songs do not appear to be added in any sort of order.
After this I get a message that the song that caused this cannot be found: 'Attempting to copy to the disk "Charlie's iPhone" failed. An unknown error occurred (-69).' Sometimes this is followed by a similar message which says that the song in question cannot be found.
When I put my hard drive into the computer it says that there may be a problem with some of the files on the hard drive and would I like to scan and fix them, but it does not specify whether those files are music files (there are photo files, Word files, all sorts on it). I haven't given it permission to do so yet, this has not caused problems with previous i-Pods -Phones or Tunes and I don't exactly see how this would affect it now anyway seeing as the files have been re-done (burned off of iTunes and stored on the hard drive directly), but this may help work out the problem.
A few last things. There is are albums which I definately have NOT put onto iTunes or my hard drive which has appeared on my iTunes music selection and I highly doubt are in the house (Bob Acri's self-titled album containing just song 3 and Fine Music, Vol. 1 by Richard Stoltzman containing the second song), they may have been added onto the computer by another family member and just innocently found their way on iTunes and my hard drive, but they're not the sort of thing anyone in my family would listen to, so maybe that might help someone diagnose the problem too.
Also, the same thing is happening with my laptop, which has the previous update to the one I mentioned above. This would suggets that its either the new updates fault or the hard drive's fault, I would suspect it would be the former as the laptop too did not have any issues like this, or indeed at all, before the two updates.
Anyway, thank you for taking the time for reading through, and if anyone could offer any hints or tip or advice to get iTunes back to speed I would be very grateful.
Thank you!

Answer 1

Having a similar issue.  Everytime i restart itunes its like its the first time its run and wants to look for music.   Yes, please help!