I'd say your best bet is to do two things:

1. Try to exactly replicate the request sent by Internet Explorer using LWP::UserAgent and HTTP::Request (just keep fiddling with the HTTP::Request object until it stringifies in a structurally identical manner to the request sent by Internet Explorer).
   
   You may need a plugin for IE to capture the headers it sends to the server (for comparison).
   
   
2. Send a message explaining the error (and the conditions leading to it) to the server administrator for that upload script.
   
   Sometimes the administrator is listed in the error message. If not, look at the contact page on the site.

-David