If you are able to upload the file manually multiple times, it means the application is not checking the uniqueness of the file by using MD5 or SHA or any other methods. So, chances are high that the problem is with your script.
Please check the following
1. Replace the web_custom_request calls that are recorded by loadrunner for file upload with web_submit_data [with filename & path with the relevant "Submit" method name (Select View Source in the file upload page and figure out the submit method name for your application)]
2. Check the correlations once again. Record twice with the same filename and DIFF
3. Record twice by uploading the same file but to a different directory or file path. Check the correlations once again
4. Record twice by uploading a different file. Check the correlations once again
5. Verify the HTTP headers sent in your reply for the upload request. Compare it with the recorded HTTP headers If anything is missing in the replay add them explicitly using web_add_header.
Thanks a lot for all your comments and inputs.
I have checked the correlations and previous pages, they are fine.
Server logs are not available.
I have not used web_custom_request and used web_submit_data instead. I have recorded many times the same with different files and same file also. Used different recording settings also. But still at this moment its not working.