Hi John,
I'll ponder the cause. At the moment, I can't add anything to what's already been discussed.
I can help with a solution, though...
Under "Melody" on the top menu, Select...
1. Edit Melody Track
2. Quantize, Time adjust
3. Timeshift melody (ticks)
4. Use positive values to push the melody later into the song and negative values to drag the melody to an earlier position in the song.
5. Keep in mind that 120 ticks = one quarter note
6. So... from the Piano Roll view, estimate how much you need to shift the melody in terms of quarter notes and multiply that by 120.
Hope this helps,
Noel