This happens mostly in illustrator but it just happened again to me while printing a .ps booklet out of indesign and converting to a pdf using distiller.
See the image below:
The left shows my InDesign Document. On the right is the pdf that results from the save. As you can see the page boundaries are being completely disregarded when saving the pdf and everything is equally shifted down and to the right.
Here is an example of me having the same problem in illustrator:
As you can see there is sometimes zero correlation between what is on the artboard and what page the objects end up on in the pdf.
This problem also has another strange symptom, it seems to have to do with dragging images from firefox onto an artboard in illustrator. The image is place automatically in the center and all objects in the file move together in one direction. see before and after photos below:
After image dragged in:
You can even continue to drag images in and it will move in the same direction the same amount every time: