There is a Flush function in the VISA palette, but that won't do you any good. Your problem is a simple timing problem. You're assuming the instrument you're talking to provides a response far more quickly than it probably does. Remember that the computer is going to be much faster than the serial port. Here's what's probably happening:
1. You write a "1".
2. You check the number of bytes at the serial port. There's nothing there, so you read nothing.
3. You write a "1" again, since you're in a loop.
Meanwhile, the instrument has received the first "1", processed the command, and sent the response, but you missed it because you tried reading too quickly.
This has nothing to do with needing to flush the serial port. You need to slow down your program. A delay after the write will do it, but a better solution is to keep reading until you see some text to indicate the end of a response from the instrument.
Also, you really should be using the VISA functions directly. The functions you're using are actually just wrappers around the VISA functions - just open them up and you'll see. NI provided them for backward compatibility to existing programs.
