It might make sense to consider transfering data in larger segments. Try seeing what data transfer rates you can get when sending larger chunks of data from your digitizer into your PC. This might actually get you a higher overall baudrate, even if each individual transfer takes longer, since you are minimizing the number of I/O calls to make to your bus. Does this improve overall performance in terms of total bytes per second?
Which bus are you using to tranfer data into your system? GPIB? Serial?
Jarrod S.
National Instruments