I am having the same issue on a 5.1 site. Host Portal works fine. Several other portals Alias works fine. Two portals on the same installation have this redirect loop you describe.  I see nobody has posted any more information.  I've checked DB Portals, PortalAlias, web.config.  Nothing out of sorts.  What is really frustrating is the portals that do work, we do not see any settings different from the portals that redirect back to the Host portal.  No errors in the error log. I created a new portal, added an alias, and that works just fine.  Same installation.

For me, this started when we installed the iFinity URL Rewriter.  I've used it on 4.9 and 5.0 sites successfully.  Unfortunately, we did all the work setting up this host and the first full website.  Then we installed the URL Rewriter.   The DNN Friendly URL was not handling the RegEx the way I wanted it to.  As soon as I get this portal issue resolved I'm going back to the DNN Friendly URL.

Thanks

Dave

Well, I resolved my Portal Alias issue.  I added another portal, got that working properly, then set the Portal Alias that would NOT work to the new portal.  That worked just fine.  So it validated the IIS side of the equation.  Further, it helped me isolate the issue down to DNN redirecting the Alias back to the Home Portal.  The interesting thing is, once I validated the Alias would load a new site, I removed the alias and put it back to the original portal that kept redirecting.  Voila!  Whatever DB foreign key was orphaned, was now deleted and resolved. 

If you are experiencing this issue.  I suggest setting the Alias to a different portal, verify that works, then put the alias back on the originally intended portal.  Obviously, you will be removing the Alias from the each portal as you "move" it to different portals.

Hope this helps...