Seems a storm in a teacup. I'm running windows 8 and Linux Mint with SugarSync and Box. I'm a SME personal user and I had this problem until I turned off Trash and versioning and after that it worked perfectly for me. A couple of things I noticed though. Copying files from Flash Drive between Linux and Windows, which I do on occasion, when I'm offline changes the time stamp, even though it shouldn't. It took me a while to,figure this out.
To get rid of timestamped files in SME is simple though, just empty the Trash.