bunbury, since I cannot predict what custom fields may exist in any given WordPress setup, and what they are used for, currently Indexy doesn’t highlight data in custom fields by default.
However, if you are not afraid of diving into the code, inserting a simple add_filter() call may be all you need to get it to highlight custom fields (or anything else, for that matter). All it takes for Indexy to highlight post content is the following line:
add_filter( ‘the_content’, array( ‘Indexy’, ‘highlight_post’ ) );
Alternatively, in your theme, you can wrap anything you want highlighted in a call to the same function:
echo Indexy::highlight_post(“whatever you want to be highlighted”);