The LPC21xx series have two JTAG ports. By altering the device's internal configuration registers you can switch to the second port, which is necessary if you want to use the pins used by the first JTAG port for something else.
However, on reset, the device has the first JTAG port enabled, so you need your own software to reconfigure it at startup if you want to use the second port. In designs using the second JTAG port, you'll need to have access to either UART0 or the primary JTAG to initially program the device.