The position: static; in this rule causes the issue:

/* Fixes so pages actually print when magic scrollbar is present */
!print .main-page-frame {
  position: static;
  overflow: visible;
}

...but I don't immediately see an easy way to fix it.

@chad, does this mean there is no fix for this?
where is the file that consist of this position: static located at?

I fooled around with this and @epriestley's fix to no resolution. If you find a fix you are welcome to submit a patch.