wordpress corrupt please help!

Hi all,

I am using wordpress 3.1.2.
Everytime I am uploading more than 5 pdf files (using flash uploader)
upload fails and then when I go to the live view, it says page cannot found and all my top navigation is gone.
I have delelted all plugins and changes to default theme and tested it. still same issue.
It seems database is corrupted or deleted but all the data is still there.
Could anyone please help?