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Can you provide a bit more information? What kind of size are you connecting with the label "larger folders"? It sounds like your connection is timing out or dropping because the server is not finding the requested file(s) in a timely fashion, but because that particular resource is in use, it's not automatically allowing reconnects.
There's a lot of "can't connect" error 50 information around the 'net, so I'm assuming you're running into that as a consequence of the connection you're using stalling or being dropped for some other reason. Are the server's drives relatively well defragmented? Finding and saving stuff on highly fragmented drives can really mess up a networked save or copy.