If you are using RTS/CTS flow control, you should not be looking at the RTS state. It will always return -1. Depending on how you handle the -1 case, I could believe your LED would be either green or red (I know you said it is red) but it will never change color.
The driver itself will properly set the state of RTS, but it's just not something we allow you to monitor, because you are not directly in control of it. If you measured the RTS signal from the pin with an oscilloscope, you should see it change when you write data with VISA Write.
CTS, on the other hand, should always be returning a valid value. If CTS is set, your device is telling you that you have data to read. And if you get garbage, perhaps your instrument is not properly set up in RT
S/CTS mode?
Dan Mondrik
National Instruments