Custom ip: can't see IRQ number in system.h

Ya that interrupt being aligned to the clock is the first thing I noticed when I looked at it. I recommend taking a look at a simple component like the avalon PIO hardware .tcl file to see how it relates the interrupt to the slave port. I think you might be relating it to the clock input or nothing at all in your hardware .tcl file and that might be the culprit. The reason why it needs to be related to the slave port is so that software knows which slave port it's going to be accessing to clear the interrupt (imagine having multiple copies or a component with multiple slave ports and that's why this is necessary). So I think due to a lack of that associating when the system.h is generated when it comes across the slave port it doesn't think that there is an interrupt paired up with it.