Got it.I also said this in post #3. I cannot say why the signal is hanging at 2.7V for 13 milliseconds. If I had to guess, it looks like you have TWO driving sources on that line. We had a somewhat vulgar expression for that when it was two TTL gates, which had the property of weak drive in the HIGH state and strong drive in the LOW state. This should not be happening unless the Xilinx part is trying to drive the INIT_B line simultaneously. There should NEVER be a reason to have both a pullup and a pull-down on the same line.
Since I'm not there and don't have access to the documents you're going to have to dig around a bit. If the docs convince you need one of them, I would go with the pullup.
Thank you for explaining.
I will try to remove the pull down and do the test again,
if necessary(if the waveform is weird or anything) I will try mounting pull up.