I had the same problem and the following worked although I don't know why! (Back up your current iTunes Folder first just in case!!)
Open iTunes (i just got various files apparently stored in iCloud). Then select iTunes/File/"Add to Library" and navigate to your external iTunes Media folder location (not Library file - which btw was greyed out and not selectable) and select "Open". A window appears indicating that Apps are being moved and replace or not etc. I was worried at this point but decided to persist. Then other files were 'moved' but in fact they were not (default iTunes local folders did not change/disk space not used) and eventually my media library appeared in iTunes 11.
As I said I am not sure why this worked or what will happen when I add Apps/Media but al least I got my media available in iTunes 11. I will continue to monitor answers to this problem to see if someone can really explain what is going on in iTunes 11. PS. As a bonus my iTunes media library is now located without having to 'wake up' my external drive before I launch iTunes (a previous gripe). Hope this helps.