Most of my music left un-downloaded after sync

I have an iPhone 4S 64GB using ios7.0.2.  I am syncing with my old trusty MacBook 10.6.8 running iTunes 11.1.1
The problem is two-fold.  I connect the iPhone to the MacBook via USB and the settings are ticked to update via WiFi, I start the sync and then walk away and when I return, the sync seems to be finished, but all the music is not downloaded.  I'm talking a couple thousand songs so I'm used to waiting.  I don't sit and stare at the sync because it often takes several hours to complete, so I don't know why the MacBook and iPhone think the sync is finished. 
What I'm left with are partial files, songs with a red square inside a red circle to the right of the song.  Sometimes artwork, sometimes not.  Some of the songs have the iCloud symbol next to them, which really confuses me since I got rid of iTunes Match a year ago (just doesn't work well over Sprint and I'm not in WiFi that often when I'm out and about.)
In short, I don't know why the songs don't sync to the phone completely, and I don't know why some are in iCloud. 
How do I get the thing to just sync all the songs from all the playlists I choose?  Can I just do it all manually?  Can I choose manual sync and still backup to iCloud?
Thanks

- Reset the iOS device. Nothing will be lost
Reset iOS device: Hold down the On/Off button and the Home button at the same time for at
least ten seconds, until the Apple logo appears.
- Unsync all music and resync
- Reset all settings      
Go to Settings > General > Reset and tap Reset All Settings.
All your preferences and settings are reset. Information (such as contacts and calendars) and media (such as songs and videos) aren’t affected.
- Restore from backup. See:                                 
iOS: How to back up                                                                
- Restore to factory settings/new iOS device.             

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