The File Upload window does not do a good job of displaying error messages, so this could be the result of many things.
- Validation Rule on ContentVersion
- Insufficient Access Rights to
upload a File
- An error during trigger processing on
ContentVersion, ContentDocument, or ContentDocumentLink
You say this ONLY happens with .msg files that have a .pdf included in it, which implies that you are able to upload other files, which rules out (2). The fact that the inclusion of the PDF is needed to reproduce this error would seem to rule out (1) as validation rules wouldn't be able to reach into the content/data of file. This leaves apex running from a trigger as the most likely culprit. You mentioned you disabled a trigger on ContentVersion, but the upload of a File will also initiate triggers on the ContentDocument and ContentDocumentLink objects. I'd look there.