Clean url, necessary or redirect?

I have recently come into a position to do SEO for an established company. Their sites are all dynamically generated from a single backend. When the url is entered you a redirected to a subdirectory which houses the 'application'. In trying to build a universal backlink structure throughout the web I am obviously trying to direct traffic/build PR for the main url. Is this redirect hurting out SEO? (as I belive)
I've attached a couple spider simulator reports. For the first site http://www.comprehensiveinc.com you are redirected to -http://www.comprehensiveinc.com/compvideo/default.asp
-http://tools.summitmedia.co.uk/spider/report35b53aba9d756dfa6114663afee69d1e.html
for site http://www.discountav.com you are redirected as well; however the spider simulator did not pick that up.
-http://tools.summitmedia.co.uk/spider/report88c2712ea3c508c54aa74455079c500d.html

when http://www.discountav/dav/default.asp is entered in the simulator:
-http://tools.summitmedia.co.uk/spider/report728f4f59b494952ad07ec070086fe880.html

I know these sites need a lot of SEO (and DAV needs some design work), your help is much appreciated.

Thanks for your help, its much appreciated!