Regardless of where the files are physically stored, any operating system (Linux, windows, OS X, etc) looks at where it *thinks* they are and then decides to read / write the file to a new location, or to merely rename it to the location.
In this case, the mount points are different for the input and the output. Linux (and windows / OS X) doesn't realize that the source and destination are actually on the same physical hard drive. Hence why it does the read / write instead of a rename. Its just how all operating systems operate. I'm not familiar with filebot, so I can't tell you if you set the same mount point for your input and your output if it will work (ie: use different folders within the mount points)
Thanks, that helped me solve my issue. I just stopped using the input folder, grabbed files from output and renamed to output. No more waiting.