When I organize my files (Manage File -> Organize File) it renames the files successfully but when it re-updates the collection it can no longer see them even in the Files pane. They still exist because I can see them in Nautilus and play them in other players. Has anyone else had this problem or does any know how to fix it as this (believe it or not) was one of my favorite features (not including the OSD and Global Shortcuts).

Same exact problem, no solution yet though.  Anyone?

Can't say I've ever run into this problem. My music is on multiple nfs shares, as well as local, and I use the organise feature on a regular basis. Probably the only differences are that I run pure kde, and use a source distro, rather than precompiled binaries.

One thing you could try is backing up/deleting ~/.kde/share/apps/amarok/collection.* and ~/.kde/share/config/amarokrc then letting amarok rebuild its collection from scratch with a clean config.

No luck.
I tried replacing those items but it didn't do anything. However, a few weeks ago, it worked temporarily and I could see my music perfectly in Amarok and I thought it was working again but this only lasted a few days.
If it helps anyone, I'm running it in Feisty Fawn and I'm pretty sure I downloaded Amarok off the Synaptic Package Manager

I might well have the solution
What had happened for me was when amarok renamed the files it didn't add the file extension. This can be very easily fixed by adding to the end of the custom file naming scheme '.%filetype' or if that doesn't automatically do it '.mp3' (or what ever format it's in) as I'm not sure of '%filetype' works when moving or copying music into your collection. I couldn't see the files without the extensions because of course amarok filters out anything that isn't a music file in the 'Files' pane. Why it temporarily worked for a few weeks I've no idea.

My method (as last posted) is working beautifully however another word of warning as far as what file extension you put on the end. It's all fine and dandy to set your path to, say, '/home/user/Music/%artist/%album/{%track - }%title.mp3' but if you forget to change the .mp3 on the end when trying to organize a different filetype (like .flac) it can turn very nasty.

I did this with a .flac file and Amarok manages not only to rename the file but also to force change the format without re-encoding so you get left with a nasty electronic squeal where your music was when you play it with other media players. This can be nearly fixed by renaming them .flac in Konqueror but in Nautilus (as I use GNOME) it still is convinced they're .mp3s but Amarok can still play them.