In my webmaster tools account they are showing over 25k url's not found and not linked from anywhere. The structure they are showing are like combined paths for 2 directories or they are adding in a duplicate directory within the structure. Like home/dir1/dir1/page.htm and this is the same for all 25k. I don't have my site linked this way or link to any of these pages. What could be going on here. Also my crawled pages per day sunk to almost nothing the past week.
One thing you can count on - there is a technical error here, either on your site or in Google's indexing. I know you said you do not have your site linked this way - I would add the word "intentionally" to your statement, because all kinds of funny things can happen.
I'd suggest using Xenu Link Sleuth to crawl your site and see if it runs into any malformed URLs.