I assume you mean that the second side of any sheet is misaligned from the first, no matter which program you use to print from. So, if you printed pages 1 and 2 from a doc to one sheet, then printed pages 2 and 3 to another, the versions of page 2 would be different.
If so, it would have to be the alignment within the printer.
It would be worth cleaning the rollers used to move the paper around, especially the pick-up rollers. They are usually covered in a slightly spongy rubber-like material. At work I always found a moistened paper towel (from the Gents) ideal for this. Slightly rough, and cheap! The hard part is reaching inside the guts of the printer to where the makers hide them. Many brands have online manuals to guide you to their discovery.