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... and added two PIOs with 32 bit I/O Width. The first as an output port (named GPIO_0) and the second as as an input port (named GPIO_1). Then I generated the system in the SOPC-Builder and started compiling it in Quartus II 6.0. After compiling it, I checked the pinout file in the compilation report and found that the output pins of the Cyclone II chip where mapped to the according pins for GPIO correctly
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In your post, you state that you made the GPIOs as input/output, but it was not clear whether you connected them to input/output
pins in Quartus. The different pin types function differently and will not work correctly unless you use the corresponding pins.
If this is done correctly, it will also show up in the Pin Planner in the Direction column.
If this is not the problem, I would suspect (since this is a development board, DE-2) that someone using it before you may have blown the IO by connecting it wrong. (I've actually seen users directly connect low-voltage IO to AC line voltage and wonder why it did not work anymore.) The boards have buffers to stop the damage from getting to the FPGA, but not without damaging the buffer.
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