I had this problem as well - the underlying problem it seems is you can't edit the androidManifest file with Phonegap Build - all you can do is edit the config.xml file which really only allows you to change a limited subset of settings.
What I would like (and a lot of others have been screaming for a long time fo) is to be able to change the windowSoftInputMode.
I did however find a solution to my problem - which was the keyboard appearing over fields at the bottom of the screen which I think is the same problem you're having.
For me - I'm using the latest phonegap 2.7.0 (but was able to reproduce the same behaviour and solution by specifying phonegap 2.5.0 in the config.xml file)
The solution I found was to change this setting in config.xml
<preference name="fullscreen" value="false" />
This does mean you get the 'status bar' at the top of the screen.. which is no biggie for me (in fact I think it's better to have it there.. at least for my app) - with that setting set to "false" instead of "true" - the page now scrolls up to reveal the field you're editing when the keyboard opens. (to be more precise, I believe the viewport changes rather than scroll up)
Hope that helps and solves your problem.. took me hours of searching and fiddles to get it to work (if I didn't find that I would have had to abandon phonegap build)
joy!
Dylan
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