You say that in Modelspace it is aligned perfectly, which begs the question,
If the UCS in your modelspace is something other than WCS, you would experience a different perspective (either slightly or wildly) in your
newly created viewport.
Another possible scenario might be that your Modelspace view is set to PERSPECTIVE view as opposed to PARALLEL view.
Try entering PERSPECTIVE at the commandline and making sure that it is set to ZERO.
Are you at liberty to post the drawing, or a very stripped down version of it, which is all it would take to debug the problem?