Can you modulate and demodulate your packets in a single VI without the USRP driver?
How long are the packets you are sending?
How long are you acquiring for?
Are you missing the same packets every time you run the VIs or is it random?
What kind of USRP are you using? (I am assuming it is either a NI-292x or NI-293x) If so, these devices are software controlled so all of the processing of the data is done on your computer. If the computer or Ethernet connection is slow it could lose packets as the computer will still be processing data before it can make a call to collect data from the USRP again. You may need to acquire for a shorter amount of time if you can.
Overall it is hard to tell what is going on without a clearer picture of what data is being received and transmitted. Take a look at the data and see if there is anyway you can make how much data you are sending and processing into a leaner process.
Noah | Applications Engineer | National Instruments