When you run FTPSync for the first time, it will transfer all the files from source to destination. The reason for this is the way FTPSync determines files that should be transferred, which is done by comparing the snapshot of source directory from previous transfer with current state of files in source directory - files that do not match are considered changed and will be transferred. When you run FTPSync for the first time, no snapshot from previous transfer is available, thus all files are considered changed and will be transferred.
If you are sure that your source and destination are in sync and would like to avoid this initial transfer of all files, there's an option:
FTPSync will run a full transfer in "simulation" mode - everything will be as if you are doing a full transfer, but no files will be transferred.