href items being “redirected”

I upgraded to WordPress 3 two days ago and have had some problems ever since. Site is dowlenroad.com.
Wordpress is loaded in the directory dowlenroad.com/Wordpress. I am using a Studiopress theme called tubular light.
Since the upgrade linked references to pages and media contained in pages or posts have been “redirected”.
Example:
dowlenroad.com/Wordpress/?page_id=854 is changed to dowlenroad.com/WordPress/?page_id=854
Obviously that causes a 404. I have checked Settings>General and Permanlinks, checked theme options, deactivated plugins, etc. Nothing helps.
I copied media from WordPress/wp-content/uploads to WordPress/wp-content/uploads as a workaround but that doesn’t change the page and post references.
It seems to only occur in a href link, but I had a user call last night to say that when he entered the password in a secured post it didn’t work: took him someplace strange.
May be a database problem, but could sure use some help figuring this out.