I was looing at my httpd directives and noticed a difference in them. I had virtualmin configured for me and noticed that Domain 1 directives are different from all new ones that I create (like domain 2 below). What exactly is the difference here...I do not fully understand it. If I delete Domain 1 and recreate it then it is created like Domain 2. I was trying to setup aliasing and got it work on Domain 1 but could not get it to work on others...it is at that time I realized the different directives.

DOMAIN 1:
<Directory /home/domain1/public_html>
Options Indexes IncludesNOEXEC FollowSymLinks ExecCGI
allow from all
AllowOverride All
Action application/x-httpd-php5 /cgi-bin/php5.cgi
AddType application/x-httpd-php5 .php5
AddType application/x-httpd-php5 .php
</Directory>

DOMAIN 2:
<Directory /home/domain2/public_html>
Options Indexes IncludesNOEXEC FollowSymLinks ExecCGI
allow from all
AllowOverride All
AddHandler fcgid-script .php
AddHandler fcgid-script .php5
FCGIWrapper /home/domain2/fcgi-bin/php5.fcgi .php
FCGIWrapper /home/domain2/fcgi-bin/php5.fcgi .php5
</Directory>

It looks like for Domain 2, FCGId had been enabled in the Server Templates.

I'm surprised that it would effect aliases, but if you'd like to test that out -- you can disable FCGId by going into Server Settings -> Server Templates -> Default Settings -> Apache Website, scroll 2/3 of the way down, and you'll see "Default PHP execution mode".

You could try changing that back to "CGI Wrapper" to see if that resolves your issue.
-Eric