I had the same issue. All my music was saved on an external hard drive. When I upgraded the most recent iTunes, it seems that all my files were transferred to iCloud. They are GONE from the external hard drive. I've started to download everything from iCloud again, except that about 1/3 of my songs are greyed out, with the "Available for Download" iCloud icon but "Waiting" status and no option to "Make Available Offline." I've tried:
1) restarting iTunes with a previous library
2) restarting iTunes, pressing "Option" and making a new library and forcing a full re-population from iCloud
3) toggling "iCloud" on and off in Preferences
4) "Updating iCloud Music Library" from the menu bar
NOTHING seems to force those songs to go from "Waiting" to "Available".
I can't delete them all and try again, because, as I mentioned, the back up copy of everything on my hard drive was removed when iCloud took over.
Has anyone else had this problem? Any solutions?