We've followed up the error from the original poster and it's simply that the google apps domain of the user's account has turned off support for third party Drive Apps. There is nothing we can do about that from our side.
The syncing of a single PDF is clearly different. We chose to save the annotations right to the PDF by default. So we need to upload the PDF to Google Drive when it changes. The PDF standard and our implementation supports incremental updates, i.e. in principle we could just upload the new or changed annotations. However, Google Drive does not support incremental uploads so we need to upload the whole file. As a consequence of this we turn off the automatic syncing for bigger files.
Another issue might be that there are times when Google Drive is slow. We experienced one period of almost a day in November or December last year when uploads and any other changes to Google Drive where extremely slow and uploads took minutes instead of seconds.