I've just tried the v1.3 script, with Avmode set to ndfltr and I don't seem to be getting overexposure (just shooting a bright scene outside the window).
2013Dec09 07:15:03 KAP 1.2 started - press MENU to exit
2013Dec09 07:15:03 CHDK 1.2.0-3155-0
ixus110_sd960 101d Oct 13 2013
2013Dec09 07:15:03 Tv:1/1250 maxTV:1/2000 exp comp:0.0
2013Dec09 07:15:03 Av:4.0 minAv:2.8 maxAv:8.0
2013Dec09 07:15:04 ISOmin:100 ISO1:400 ISO2:800
2013Dec09 07:15:04 AvM:2 int:2 Shts:0 Dly:0 B/L:0 USB:false
2013Dec09 07:15:17 1) IMG_1214.JPG
2013Dec09 07:15:18 meter : Tv:1/500 Av:2.8 Sv:80 774:774
2013Dec09 07:15:18 actual: Tv:1/1250 Av:- Sv:200
2013Dec09 07:15:18 AvMin:2.8 NDF:NDout foc:infinity
2013Dec09 07:15:24 2) IMG_1215.JPG
2013Dec09 07:15:24 meter : Tv:1/200 Av:5.6 Sv:80 845:845
2013Dec09 07:15:25 actual: Tv:1/1250 Av:- Sv:120
2013Dec09 07:15:25 AvMin:2.8 NDF:NDout foc:infinity
2013Dec09 07:15:32 3) IMG_1216.JPG
2013Dec09 07:15:32 meter : Tv:1/200 Av:2.8 Sv:n/a 719:719
2013Dec09 07:15:32 actual: Tv:1/1250 Av:- Sv:320
2013Dec09 07:15:32 AvMin:2.8 NDF:NDout foc:infinity
Exif values:
IMG_1214.JPG - 1/320, f2.8, iso 50
IMG_1215.JPG - 1/500, f5.6, iso 50
IMG_1216.JPG - 1/1250 f2.8, iso 320
IMG_1217.JPG - 1/1250 f2.8, iso 250
A subsequent test of 6 shots gives exif showing 1/1250. I'll strap it to the copter and give it a proper go this afternoon if I can sort out my GPS issues...