RA Eletro,
I think the problem is related to using VISA Move In 8 over a remote VISA connection. The utility to load a VI to flash verifies that the load to flash was correct by reading it back using VISA Move In 8. In some cases, this can be very slow. This might be corrected with the latest version of VISA.
As a workaround, put the card in a windows machine to download to flash - local or remote. Boot your controller into Windows (remove the floppy) and load the VI from windows on the controller.
Regards,
Chad H.