Do you run on a shared server? It could be that there is too short a time on the PHP time out and I've know shared servers time out if they haven't been able to process the file quickly enough.
You could try navigating direct to the main AdminCP folder file for Threadmins to check that it has uploaded where it expects. That would be the ACP location plus
/userthreads.php.
You might want to try uploading the XML to a folder on the server and then importing it from there and see if that helps.
If you want me to take a look after trying these suggestions, I'll be glad to. Just PM me the URL and account details (a new account if possible with full admin permissions) and I'll take a look. If you could verify for me that you have a database backup before I started doing anything that would be ideal.
Matt