Timeout during folder scan

I have a scheduled job that transfers a 6GB zip file every night.

I decided to break up the file and just transfer the incremental changes in the included data. So it is a 6GB folder/subfolder layout, all files are 3MB or less.

The job logs in to the ftp server fine and starts to scan the folder structure, but the structure is so large that the transfer times out before any files are transfered.

Does anyone know what would cause this or how I can start to examine the problem further?

Thanks!