I have a fix, but it's not the right one.
I'm using the original java line in the auduino shell program.
I executed the cmd "sudo -ln /dev/ttyACM0 /dev/ttyUSB0
I'm using the /dev/ttyACM0 as the Programming port. I now have /dev/ttyUSB0 because of the symbolic link.
The LED Blink program compiled and ran successfully.
The Port no longer says COM1.
and the preferences no longer keep resetting to COM1.
serial.databits=8
serial.debug_rate=9600
serial.parity=N
serial.port=/dev/ttyACM0 (Was COM1)
serial.port.file=ttyACM0 (dunno what it was, but it wasn't this)
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Serial Port monitor worked when I uploaded ASCIITable.