When I enter sub1.main.com on the browser url line, my index.php page to the project is loaded correctly.
Is this a mod_rewrite (.htaccess) change or a Zend Bootstrapping issue?
If all your URLs are relative in the page, and not absolute, then it's most likely the browser causing the problem, not the web server.
If you go to www.example.com all relative URLs will default here unless you add a base href to the page pointing everything to subdomain.example.com, which will then try to load images and everything else relative from the subdomain.
If you go to subdomain.example.com, all relative URLs will default to this subdomain instead.
Sounds to me like you're accessing www.example.com and need to use absolute URLs directing the links to subdomain.example.com to solve your problem.