I am using some custom PHP in certain pages/posts on my site.
The code is inserted into content using "Shortcode Exec PHP" plugin, and I actually reference from it some functions in custom_script.php from my regular site theme.
The problem with this was that WPTouch can't find those functions and rendering thus failed.
The workaround was to place this in wptouch.php, @ line 35:
require_once ( get_stylesheet_directory() . '/custom_script.php' );
I guess this is OK but it would be nicer to have some hook to include any additional code.