Ok, a little bit more info. It seems that this only happens when syncing via WiFi. All deleted songs or podcasts still show up (broken with a "!" if I try to play them from iTunes) when syncing over WiFi, but as soon as I connect the phone directly to the computer with a wire, the initial sync gets rid of all the dead entries.
I had exactly this problem recently. More in desperation than anything I recreated my iTunes Library files using the instructions at http://support.apple.com/kb/HT1451 and to my surprise it solved the problem. Unfortunately I had to re-sync all my music and playlists, which took some time, but in the end it was worh it.
See if this helps/works for you:
- Eject your iPhone from your system, and close iTunes
- Either reconnect your iPhone and let iTunes launch or launch iTunes and connect iPhone.
- Let everything “sync”
- At the very top left in iTunes directly unite the red yellow and green buttons you’ll see a music note, a video clip icon, a monitor icon, 3 horizontal dots, and an i’phone icon.
- Click on the iPhone icon and there will be a check mark at the top to the left of “Sync Music”. Make sure that the “Selected playlists, artists, albums, and generes” radio dial has a dot in it.
Now here is where you need to look closely. . .
Underneath the header summary there will be 4 or 5 different trays/boxes/columns listed as follows reading from left to right, and top to bottom:
- There might be a 5th at the bottom of all that titled: “Manually added songs”
You can select and delete/remove those songs if they appear in the “manually added” tray.
ALSO. . . In each of the other trays/boxes/columns, be sure to hover your mouse pointer over EACH OF THEM and scroll through the lists because there might be a checkmark next to something that is causing certain songs to “reappear”.
Let us know how you make out.