We have a sharefile Enterprise setup where it mostly works, we have problems though that download and upload doesnt work from certain folders in our shared setup. The error we get is "Service unavailable. Please try again later".
On an Enterprise setup, are those specific folders hosted on the cloud or on-premise? If the former, it could be an issue with the cloud storage location being blocked by network settings. If the latter, it may be an issue with the StorageZone setup.
I had similar issues when I setup my on-premise controller with tech support a couple of different times. Somehow, something on the backend, outside of my control, got munged due to the 2-3 re-installs we did. It took them several days to track it down, but when they tweaked it, it all worked.