Sometimes devices like that use pins like DTR (Data Terminal Ready) which trigger an interrupt and track the time between interrupts and decode that rather than actually feeding data in to the serial port on the data lines.
(edit: The software might be polling a line in software rather than relying on a port to have something interrupt on one of the pins. DTR and RI, ring indicator, are still the likely suspects. Power to the device, likely an IR phototransistor, is likely to be from driving one or more of the extra pins to +12v. See: http://www.tldp.org/HOWTO/Serial-HOWTO-19.html)