Do redirected to other pages in CMS hurt ranking?

I have a lot of inbound links, but I redirect them immediately...

[drshields]

Last week, I finished my CMS implementation; I'm starting to regret it because it doesn't make my job all that much easier, but that is a different post!

Here is what I am wondering: I have lots of inbound links from other sites; they link to 'mysite.com' - however the index.php on mysite.com points to 'mysite.com/cms-directory/news/news.php' or whatever the page may be.

My Question: Because the other sites are not pointing to the long url that my pages now have from the CMS, will they ever get the benefits of having inbound links to the site? They've already lost some SERP (I was prev #1 in google) but I'm hoping it comes back.

Thanks.