I know this sounds obvious, but I think I may be able to offer some more evidence to support this, and that is that the SMS software is overriding the registry.
As my TP1 gets squirrelier, I've noticed that the SMS app has developed a bit of an attitude about when I'm allowed to turn my screen off. If I turn off my screen too soon after sending a text, for instance, it turns the screen back on. Sometimes it does this a couple of times and we go to war. Other times, when I try to turn the screen off, it simply refuses and just stares back at me as if to tell me it will no longer serve me but I will serve it.
It's actually a bit like Washington.
Anyway, I think a possible resolution to the wake on SMS on the TP1 and possibly the TP2 (as well as the XV6700) is to deal with the SMS software itself.
I'd be interested if those using other ROMS sans this SMS or who have removed this SMS software and replaced it with another are still having problems.