It's the same UART (UART1), but it's run through the MUX/SHIFT part and if we are lucky the interrupt is on one of the GPIO pins that can be muxed in.
The tricky thing is that the headers etc. in the Arduino environment might modify the mux settings when you start using the Serial2 (I think that's the object in Arduino env. corresponding to the UART1).
One check to do is to simply hook up a terminal to the UART1 header next to the ethernet jack and see if there are any conflicts with the interrupts. By default it's hooked up to the console in Linux, but when you start using it in Arduino it disconnects the console.
Digging into the code in the Arduino env. regarding interrupts and serial might also reveal something, mainly of they share pins deeper in.
/Thomas