same problem here. the first client syncs the library. all files look good on the web interface, but randomly some files can't be downloaded from the web interface "invalid file id" is the error message.when i try to download the library on another client (windows 7 or windows 8.1), i got the "Failed to get file information from remote library" error message (because some files are missing).
when i manualy reupload all defective, missing files through the webinterface, i can also download the the library from the other computers. it looks like a nasty bug while uploading.
i have a clean 3.0 install on the client and on the server with nginx, ssl on 64 ubuntu 12.04