c2c_get_current_custom() relies on WordPress's
get_post_custom_values() function. The latter performs a query without specifying an ORDER BY clause in the SQL, so the order of the data returned cannot be depended on (as you've noticed).
Presumably you'd expect/prefer the custom field values to be ordered alphabetically?
In thinking about it, it seems like it may be worthwhile for me to allow specifying an 'order' argument to a few of the functions. In the meantime, there isn't a straightforward solution for you. Depending on where and how you're using the function, you can invoke the output formatting function directly with the sorted custom field values.
For example, Instead of something like this:
echo c2c_get_current_custom( 'myfield', '', '', '', ', ' );
$cfvalues = (array) get_post_custom_values( 'myfield', get_the_ID() );
sort( $cfvalues );
echo c2c__format_custom( 'myfield', $cfvalues, '', '', '', ', ' );