I think I've found a bug in the C library last year, I think it is time to get it confirmed.
I am using the Pi with 2 boards. While using it, I found out that wierd stuff was happening: bits were toggling on the order board, while handeling commands to the other.
Diving into the code, I found in IOPi/ABE_IoPi.c that the variables portaval and portbval (and others) are NOT per board. So when I change a value for board (e.g. at address 0x21), this value will also be written to a different board (e.g. at address 0x27)!
I've made a quick fix and made arrays of portaval, portbval, etc, so each board has its own variable.
I didn't see th problem anymore after this. Am I overlooking something?
What I still see actually, is that sometimes when toggling an input, it seems to give a side-effect and toggle another output pin. I have to debug this further, probably has nothing to do with your board. But if it does and you might have an idea, I would love to here about a workaround/fix!