Maybe it's your browser. I found that I could not upload PDF files properly with Opera (v7.23 for Linux). It would put them in the /var/site_access/storage/original/text directory instead of the /var/site_access/storage/original/application directory. There would be a link, which pointed to the correct directory, but the PDF file wasn't there.
Using another browser (Mozilla, Konqueror, IE) worked fine. Other types of files (e.g. OpenOffice, MSOffice) didn't have this problem.
I had a similar problem - don't know if this will help you, but it might save someone from some trouble.
First, there are two config files that determine the size of the file you can upload. You want to check /etc/php.ini for "upload_max_filesize" and "post_max_size".
You also need to check /etc/httpd/conf.d/php.conf for "LimitRequestBody".
If the LimitRequestBody is too small, you will see an error in your apache error_log, so that's pretty easy to diagnose.
I also had a problems using an older version of php (I was using 4.2.2) - even with the all the above settings correct, I was unable to upload a large file. When I upgraded to 4.3.4, the problem went away.
What is the size of the file you're trying to upload?
