Hi,
Have you tried to upload .pdf files to CMSDesk from different machines? If it causes the same problems on all of them, it is definitely a server side issue.
If you have already tried that, we could continue troubleshooting if you could send us an e-mail to support@kentico.com and give us access to your site so we could reproduce the issue and test it directly on your site.
Thank you.
Best regards,
Filip Ligac