As well as with the arrow keys normally used, image-alignment may be altered from this menu option or all alignments may be reset.
By using 'Shift+ArrowKey' you can make adjustments of a single pixel.
The size of the pixel-step may be set in 'Edit/Preferences' and the default-value is four pixels.
Any vertical alignment differences are errors that should be corrected with these controls.

Put on your red/cyan glasses to view these images :-

This is the image-pair before any adjustments have been made. There is vertical misalignment.

Vertical disparity reduced with the up/down arrow keys or menu options