Did some more digging to find that if you navigate to the sub-portal alias without the www in front of the domain, ALL links work properly.
If I place a www into the url, and then click to a page, the sub-portal folder get's dropped from the URL and the resource cannot be found.

So clicking on the About Us page for
http://schooldistrictsite.com/highschoolsite
results in being taken to
http://schooldistrictsite.com/highschoolsite/aboutus.aspx

But clicking on the About Us page for
http://www.schooldistrictsite.com/highschoolsite
results in being taken to
http://schooldistrictsite.com/aboutus.aspx (Notice the missing highschoolsite sub-portal folder)

One other thing... The primary portal schooldistrictsite.com only has the portal alias www.schooldistrictsite.com and not a portal alias of schooldistrictsite.com (no www).  But even when I add the portal alias schooldistrictsite.com (no www) to the aliases, the site behaves in the same manner as described above.

Any ideas?  I've been struggling with this for awhile now.

Thanks again.
www.schooldistrictsite.com/highschoolsite