One thing i will say is i am not a fan of the live view for it focus, i always feel it's off dont no why but i have noticed this in a few shots. I now only use it for family snap shots.
I don't understand this (not specifically your post).
As far as I understand it, the OP put the camera on the tripod, then used live-view to ensure that the manual focus was good.
I assume they zoomed in and confirmed the position.
With live view, my understanding is that the camera sensor is 'reading' the light, and then displaying it on the LCD [instead of writing it to card].
When the shutter is triggered, the curtain should rise, the aperture should move to position, then curtain 1 falls, then curtain 2 falls.
The light hits the sensor, then gets written to card.
How can the focus change? What can be causing the light that was in focus to now not be in focus?
Only the aperture change, but the camera would perform this anyway. Ok, so the shutter moves one extra time.