There's been half a dozen threads like this recently.
In short: no, CHDK can't help in you trying to brown out the camera by making it work from lower voltages than its capable of. Yes, some models (a570 and a590 to name the top from recent posts) seem to sometimes shut down trigger happy even if CHDK tells you the batteries are at 2,4 V and the blinking battery warning icon is mightily annoying as well.
Yes, you need a different set of batteries or/and a better charger, and before that you may find help from cleaning your battery contacts.
If the batteries go below 2,0 V according to CHDK even when you know there's 60 % charge left, the batteries are not suitable for use in a digital camera even if you can still draw current from them in some other, lower current device. 1 volt per cell from a NiMH (I'm making an assumption here from your start voltage...) pretty much equals an empty cell.