I have this exact same problem. Only one DWG file will upload (without attached x-refs).
When I try to upload DWGs with attached x-refs, I get the error "Server threw an exception." I tried contacting support, and they weren't able to provide a solution.
I am perplexed - neither of these problems occurred until I installed the latest version of Buzzsaw... I tried re-installing, and that didn't work. This is very frustrating when you need to upload 300+ drawings!
I also appreciate any help that can be provided.