When reading the article again, I see that you indeed wrote "suspend to RAM".
My fault probably was that when reading an article about a phone and OMAP3 I was implicitly thinking N900. And as far as I know N900 does not use suspend to RAM at all.
So obviously your GTA04 software is more advanced in that respect.
I have no idea what is the state machine of the various OMAP domains with respect to those power management states when you wake up from suspend to RAM. But I'm quite sure that not everything is fully active instantaneously after the first pulse on the interrupt line. Whether the reason for the missed interrupt is buried somewhere there?