Music not restoring from backup during new iPhone 5 setup

Quick question.  Recently puchased iPhone5 and need to transfer everything from old iPhone4.  I've performed a manual backup in iTunes.  When connecting the new phone and selecting restore from backup, it restores everything but the music and the playlists.  I have no idea why.  This process worked with my phone, but when it comes to my wifes the music never restores.  The only difference between the 2 devices is that she likes to manully manage her music, so the sync only checked items and the sync music boxes are unchecked.  I don't see why this would prevent the music from being backed up though.  Any suggestions?

rockmyplimsoul wrote:
Instead of manually managing the music on your iPhone, manually manage the contents of a playlist and auto-sync to that playlist.  You're doing the same thing, just managing a playlist instead of your phone.  The beauty of this is that you never lose track of what you manually chose to sync to your iPhone.
Oh that's what I do now, lol. I just (naively) assumed that my phone was doing that for me, so to speak. When I first put music on my phone (manually) I assumed that if I manually synced my music, the information relating thereto would be included in my backup data. If I had known it wasn't, I would have dumped all my songs into an "iPhone" playlist and then copied that playlist to my phone. Problem solved. I just didn't know that at the time.
iTunes, and Apple in general, does so many good things that this clearly isn't a huge complaint. But it strikes me that most people who manually selected their "iPhone" music probably don't want to "lose" that carefully selected music when they upgrade their phone. And maybe I'm an idiot but it took me a little digging to wind up here to find out why my music hadn't transferred, and how to go about "rectifying" it (ie you bloody can't, really, you just start anew).
Maybe I'm asking too much, but I find it strange that there isn't an import feature on the iPhone - provided the corresponding file is found on the iTunes being used. Especially since it's the same computer the phone is synced to, to begin with. A) I'm giving music to myself, B) I'm not even giving myself music, because I already have the corresponding music in iTunes, so there's clearly no threat of file-sharing. Barring that, maybe a warning when you choose to manually sync music to your phone. (Apologies to Apple if I'm wrong, but I don't remember seeing one.)
Again, this clearly didn't ruin my life, but everything on my phone synced seamlessly except my music. It only took me 15 minutes or so to recreate my iPhone playlist, but it took me a good hour to figure out why I had to (and how to avoid having to in the future). It was a strange hiccup from a company that pretty much always makes my life easier (unless I need to run Flash).
In the end I got to read a bunch of Allan's posts, which did provide some entertainment

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