Sorry for the late reply. I've eliminated the virtual machine, here's the output from the command:
Output from server-01
PPBE does communicate through a USB to Serial Port adapter, but not through the normal serial port on the real machine with 12.04 installed.
root@server-01:/working# dmesg | grep tty
[ 0.000000] console [tty0] enabled
[ 0.334182] serial8250: ttyS0 at I/O 0x3f8 (irq = 4) is a 16550A
[ 0.560728] 00:08: ttyS0 at I/O 0x3f8 (irq = 4) is a 16550A
[ 20.112596] usb 4-2: pl2303 converter now attached to ttyUSB0
PPBE appears to be written in java, and the installation includes a loading a JRE into the installation folder along with it. I don't think this is important, but I've included the information in case I'm not thinking of something.
My current line of thinking is that there is another program on server-01 interfering with the serial port in some way. Is there a way to determine if any other programs are accessing the serial ports? What are your recommendations and suggestions?