Hello ceties,
If you download and install NI-Serial 3.1 there is a property node in the Serial functions pallette that specifies the number of bytes available at the serial port under Instrument I/O>>Serial>>Bytes At Port. With this you will be able to know how many bytes are left on the port and then determin if it is empty enough to send the next command.
Daryl E
National Instrument
Applications Engineer