No issues for me either.
It is a website limitation. If the desktop client had an easy way to specify folders you'd like synced then obviously it wouldn't be an issue, but I couldn't find a way to do that.
I had my hopes raised tremendously by Amazon Drive, as being able to store stuff in the cloud and remove the original would save me terabytes of space. Which I would only consider because files can be played within the drive interface. But uploads are super slow, files larger than 2GB must be synced and can't be played online. Such a shame.