Some experiments copying songs with my iPhone 4s with Manually Manage Music activated:
Thinking that the issue are related with the Smart Playlist I have deleted all the Playlist that I have before except 2: One with the songs with more than 3 stars with 443 songs and one with the songs played minus than 1 time with 6316 songs.
Times to copy:
With 2 Smart Playlist with 443 and 6316 songs with Realtime Update Checked
11 Songs: 1:27 minutes
10 Songs: 1:28 minutes
With 2 Smart Playlist with 443 and 6316 songs with Realtime Update Uchecked:
11 Songs: 0:17 minutes
11 Songs: 0:19 minutes
With 2 Smart Playlist with 443 and 6316 songs with Realtime Update Checked on the first and Unchecked on the second
12 Songs: 0:17 minutes.
13 Songs 0:18 minutes.
With 2 Smart Playlist with 443 and 6316 songs with Realtime Update Uchecked on the first and Checked on the second
Note: When I Check the Realtime Update on the second Smart Playlist starts a Preparing To Update operation that lasts 1:10 minutes.
13 Songs: 1:34 minutes.
10 Songs: 1:27 minutes
All the 2 Smart Playlist with the Realtime Update Unchecked again.
16 Songs: 0:20 minutes.
14 Songs: 0:17 minutes.
16 Songs: 0:19 minutes.
36 Songs: 0:27 minutes.
Checking again the Realtime Updtate on the big Smart Playlist starts a Preparing To Update operation: 1:15 minutes.
Conclusion: The issue is on the Smart Playlist Realtime Update. For some big Playlists you must wait the thme for update the Smart Playlist plus the time neccesary for copying the songs. Maybe you must multiply this time for every Smart Playlist that you have.