Please post your serial LabVIEW code. There is a strong possibility that you may be doing a little more work in the software than you should, and this could be affecting your performance.
The only difference in performance between DOS and Windows for reading from the serial port will be a result of Windows, or how you wrote the serial portion of the LabVIEW code. LabVIEW doesn't do serial IO any slower than in DOS.
I have extensive experience with Serial IO in LabVIEW and elsewhere, and may be able to help streamline your code, if you were to post it (or at least a GIF screenshot of the diagram.