Interfacing to a daughter card through PROTO"

I found out a couple of things today. First: the IO called Y8, pin 33 on J16 seems to be connected to H17, pin 35 on J11. Don't ask me how or why, but I get the same signal on both these pins. Second: IO T13, pin 21 on J16 is connected via a pulldown. This shouldn't have any effect I thought, but it actually distorts the signal a little. A square signal get a little slope on the right flank for me on this pin. IO T12, pin 27 on J16 is connected to both a pullup and a pulldown. Again, this shouldn't have any effect when a signal i applied, but even without a signal there, I get some really weird and periodic noise/signal on that pin. I also have some issues with IO W12. It almost looked like the discharge slope of a capacitor. I have no idea what might cause this.