Don't let it beat you 

IF you look at the schematic, what other chips/pins does the IRQ signal go to?

Obviously a pin is holding it 'stuck' high, your logic probe should find this.
If chips are socketed (or you socket them) you can bend 1 pin out, so it doesn't plug into the socket, and although the chip will be working you can now measure the pin itself to see if it's outgoing IRQ control to the cpu is 'stuck' or not.

You would test chip-by-chip until lifting one of the pins out of socket brings the IRQ on your cpu back to life....

Failing the pin-bend method, perhaps just lift out all chips that control the IRQ cpu pin, then replace the chips one at a time, you should see the irq 'blinking' (as you said) until plugging 1 chip back in kills it again...

Another option is that all the IRQ pins are ok, and in fact a shorted irq track on the board etc.

If you point me to a schematic/link i can help you test/prove things too.
MM.