Hi,
Usually CPU load won't affect the operation of the serial port. The low level communication protocol (handshaking, frame format, etc) is handled directly by the hardware (UART). When the serial port receives data, the driver retrieves the information in an intermediate buffer until your program requests the data.
Check if what you are seeing is a display error. When the CPU gets loaded, the graph might show gaps, but the serial data should be complete.
Hope this helps.
DiegoF.
National Instruments.