I don't know if this is your issue, but there's something I learned early on that might relate.
If you're doing anything like moving an object, resizing, placing a mask - where it needs to be in a precise location - while your preview setting is at (say) a 4X3 mode, but then you export it to a 16X9 resolution, everything you did will be out of place.
So first thing I would do is make sure the preview and export resolutions are compatible. Your preview can be at a lower resolution, but still needs to be 16:9. For instance, you could have the preview be at the lowest 16:9 setting to lower the load on your CPU and speed up the editing, but export it to a 720 or 1080p resolution.