First, I don't have a solution. Other people know more about the ixuses, but I believe you may have discovered something new. I only have my a570is which has manual focus in Canon's firmware, but as you see in the timelapse script comments I too had some problems forcing manual focus from the script. I just didn't spend much time on it because to me that feature was just to prevent me from screwing up by forgetting to set MF.
It's very much possible that there's another way, maybe even one that's already scriptable. You are forcing the camera to manual focus using a propcase. It's common that changing procases do what we wish, but that the changes aren't quite as widespread as they are when you change the same feature from Canon's user interface. The typical example is that Canon's OSD will usually not be updated by our overrides, because we aren't changing the actual software setting at the high user interface level. Instead, we are changing low level things, i.e. something that the change made via the user interface eventually changes, but not directly. So often our changes are overwritten by the original firmware without a warning.
When changing between play and rec modes, Canon's firmware executes some initialization stuff to prepare for shooting or playback. From what you say it very much sounds like that there's something that makes the manual focus mode become more strongly into effect and that it actually reads the propcase value during that process. It's possible that whatever this is could be called at will by CHDK or duplicated (not now, but in the future), but don't get your hopes up.
It's also possible that something else that we can already do in lua and/or ubasic has the same effect. For example hitting the display button (or whatever key stroke combination is needed for your camera) to disable the LCD and the sensor and then coming back from that state could cause some of this initialization to be called. I'd also test zooming in and out a step by button presses. Think about it for a while and you'll probably think of a couple of more things you can test.
Oh and changing between rec and play modes is also possible from scripts in some custom builds for some camera models (probably not yours), but I know that -- like many other overrides -- this particular way of switching is also not complete and it may skip this thing that's helping you; but can't know without trying.
And lastly, does your camera have an auto focus lock feature? If you set that before starting the script and remove all focus related things from it, what happens?
