First, Collapse the modifier so you can keep the sides that look good. Right Click the modifier on the stack and select collapse to or all and click yes.
In editable poly, choose face selection and select all of on side that isn't aligned properly.
reapply the UVW Mapping modifier, it will only apply to the selected faces.
Click the [+] next to the UVW Mapping modifier, it opens up and displays -Gizmo. Select it and you now have full control over the orange projection gizmo on your box. You can scale, move, and rotate the texture. Simply rotate it until it appears correct.
Collapse and repeat if necessary.