double check that the footprints you made yourself are centered at 0,0 on the grid, or near it, from within the footprint editor.
If they are far away from 0,0 you can get some strange positioning issues
When you update from sch new components are always placed outside the pcb area.
however this is referenced to their 0,0 center. So if the component was designed 40mm away from 0,0 this can mean they get placed 40mm form where altium intended to place them.