Most likely, the software is creating a list with the files that are going to be transferred. It's a common technique for such applications to make the upload easier or to benefit from the resume procedure in case something bad happens. Unfortunately, it's impossible to change this, unless is defined in the Settings menu. The option should be called something like "Pre-load or Pre-allocate" files.
Additionally, you can use another FTP client to transfer the files. In this case, FlashFXP is an alternative.
Application's page at Software Informer: http://flashfxp.software.informer.com/