I am using PhoneGap version 3.0.0
I had to do two things to get this working:
Firstly:
I had this set in my index.html
<meta name="viewport" content="user-scalable=no, initial-scale=1, maximum-scale=1, minimum-scale=1, width=device-width, height=device-height, target-densitydpi=medium-dpi" />
Needed to change this to:
<meta name="viewport" content="user-scalable=no, initial-scale=1, maximum-scale=1, minimum-scale=1, width=device-width, target-densitydpi=medium-dpi" />
When setting device height, my 100% heights were taking into consideration the status bar.
I then also had to add this line into my config.xml:
<preference name="DisallowOverscroll" value="true" />
Hope this helps,
Ian