There are a couple of other methods of getting files to and from your PXI controller:
1. You can use the LabVIEW FTP server and VIs to do the transfer - create your own FTP app with a progress bar
2. Use Measurement and Automation Explorer (MAX) to transfer them - right click on your remote system and slecect "File Transfer" - this option opens up a FTP interface (written in LabVIEW btw) which has a progress bar for each file you down/upload.
3. Use any third party FTP client available (try a google)