I've built two, identical, custom devices with the AT91SAM7S321 as main microcontroller. The device's ADC didn't work as expected, so I started bugtracking (again

The ADC pulls a signal line low when there's a new sample available. This signal line is connected to pin D6 (hardware pin 42, ARM pin PA30), a pin that can be used as the MCU's second interrupt line (IRQ1).
Both devices were unable to pick up any line changes, even with the simple test program below:

After that, I made a hardware bypass (wire jump) from the ADC's line to pin D3 (hardware pin 16, ARM pin PA20), the MCU's first interrupt line (IRQ0). This time I was able to pick up the line changes and everything worked as expected: a nice steady square wave on output pin C5. Doesn't seem to be a hardware problem as pin D6 does work as a normal input/output.
Trouble is that I really need pin D3 (IRQ0) for other purposes and want to use IRQ1 as interrupt input. My guess is that there's another error in one of the .h and/or .c-files, but which one? Can somebody please look into this? Thanks in advance.
Paul