This may or may not help depending on the instrument you are using. The delay with resending commands isn't just from the data transfer but also because most instruments go ahead and reconfigure, even though there is no change in configuration.
IVI Instrument drivers provide for "State Caching", maintaining the state of the instrument and only sending commands when a value changes or becomes invalid. If there is an IVI driver for this instrument then you could use that driver and avoid sending redudant commands.
For more information on IVI please refer to:
http://zone.ni.com/devzone/devzone.nsf/webcategories/5FB594A1C20D93E3862569FD0071D18A?opendocument
and
http://www.ni.com/ivi/
Regards,
Kamran - NI