I have a couple of suggestions for you, but these may not work if your instrument is not allowing for the data to be moved off the port. This could be caused if your instrument is missing a handshaking signal, for example. Two VIs that may clear the port are Serial Break.vi and Flush I/O Buffer.vi. I would also suggest using the VISA Status Description.vi after each of these calls to assist in troubleshooting. This VI can be much more descriptive than the LabVIEW error codes.
A better way to fix your problem would be to eliminate the printer from missing the data every once in a while. Perhaps some timing issues may be occurring in your program, a loop delay could possibly help.
Ryan Tamblin
Applications Engineer
National Instruments