iTunes and the Music App, I am yet to fully understand thee.
I set my iPhone to manually manage music. I copied across 5000 songs to my iPhone and after it was done, I unplugged my phone and none of the music was there!
It turns out that some quirk somewhere prevents songs from being added if I manually add songs I purchased from iTunes.
So I worked around this and only added my non-purchased songs and that was fine.
The next time I connected the phone to...