Sites linking in

I noticed inside of google webmaster tools my sites linking in

my internal site links

my main page is my domain name

but when you click on the home button anywhere inside the site it goes to

my domain name/index.php?page=en_HOME

am I being discredited as having atleast one link on every page back to my home page?

I don;t have all the infomration to answer this question fully but from what I can determine from your post,

No, I don' think you are being penalised.

Looking at the URL you posted, it seems that your site uses the Parameter in the URL to pull content in a tmeplate based manner rather than going to seperate pages. At a guess all your page links have URLs that start /index.php?

Whilst this isn't optimum for SEO I don't think it will be causing you a big problem.

There is an easy fix in the form of a mod_rewrite or 301 redirect, depending on eaxt requirements.

Why do you think you have a problem?

I noticed in " IN " links on google webmaster tools went from a ton to like 2-3.. under the inbound links / internal links it shows my main url as my domainname.. so I figured the internal ment pages of my site linking internally to my root domain.

then I remember reading the friendly google guidelines and it said atleast one link on everypage linking to the home page.

I could be wrong. but it is something I will tackle here this week. I had some issues getting the mod rewrite to work to the root domain without putting a directory behind it which is confusing me.