about component made by user logic

You beat me to that, but I would check the software stuff that I suggested first, then check the hardware timing. Another thing you can do is remove your custom hardware and reads/writes to it in your software just to make sure it's not something in the custom user interface causing it (I doubt it would cause that since I've based many designs off it without problems). But do these steps one at a time so that in the end if it gets fixed you know how you went about doing it.

Another thing worth checking is the address space for that interface. I've seen SOPC builder once take an address space of 16 bytes and bring it down to 4 bytes and that caused some nasty problems (mainly because I didn't expect that to be a cause).

Good-luck