Hi,
I couldn't find a CTS timeout error. Using VISA there is only a general timeout error. In any case, I don't think the timeout would solve what you are describing.
A timeout is the time the functione will wait for the operation to complete before returning. This avoids that the function will "hang" indefinitely waiting for the data if, for example, you forgot to connect the device.
Also, CPU load is not likely to affect the serial communication. The handshaking is done directly by the hardware. All the received data is placed in a buffer by the driver. If your program is busy doing something else, the driver will keep the samples until your program calls the serial read to retrieve the samples. If your program doesn't retrieve the samples, you'll
get an overflow error.
Check your programto see if you a over writing something. You can also log the data to afile inmediately after the read function. That way you can check is the samples are missing.
Hope this helps.
DiegoF
National Instruments.