Looks like a very interesting article, although at least I cannot get all the details at the first reading.
However, I wonder how the author can just talk about about "suspend"? It's more than 2 years that I was struggling with OMAP3 documenentation, but I vaguely remember that there were 4(?) levels of suspend. Clocks and power are controlled separately. The deeper you suspend the more power you save, however at the price that waking up is more expensive (and maybe some interrupts are completely lost???). On top of that the SoC has numerous clock domains and power domains.
Whether this complexity has its part when some interrupt handling works sometimes but not always or always only once?