You may want to see how your website cache for your homepage looks like on Google. Maybe its reading the wrong header everytime. My suggestion would be to check that 1st. If it shows fine, I dont think it will hurt your rankings as such. If you have rel=caononical in place correctly, you would be fine. It would be worthy to identify your pages where you want rankings and based on that, you could diagnose.

I would suggest that depending on the number of pages, you can either do a htaccess based redirection or an apache mod redirect.

Here is an article which could help you.

http://httpd.apache.org/docs/current/mod/mod_rewrite.html

Based on the version you have on your server, these documents would be helpful:

http://httpd.apache.org/docs/2.0/mod/mod_rewrite.html

http://httpd.apache.org/docs/current/mod/mod_rewrite.html

Please note: this is not something you would like to do unless you know Apache confuration yourself and you know the codes and its logic.

Subdomains do not pass on good link juice to your domain. As Alan rightly pointed out the value is undermined due to the fact that Google sees them as separate domains.

Have you tried apache based redirection and URL rewriting?