Hi!
when you said
Today I used the WP Media Manager which used a path that looks like this:
http://www.newscorpse.com/ncWP/../Pix/Charts/congress-media-approval.jpg
can you describe exactly what you did and how you used the media uploader? you could even take a screencast using http://screener.com
Also, have you modified the upload folder by adding the specific define( ) call in your wp-config file?
Lastly, have you deactivated the WP Easy Uploader plugin? And while we're at it, what other plugins are you using?