You need to have nested loops for flex fields inside a repeater
if (have_rows('repeater_field')) {
while (have_rows('repeater_field')) {
the_row();
if (have_rows('flex_content_field')) {
while (have_rows('flex_content_field')) {
$layout = get_row_layout();
// and the rest of your flex field output
} // end second while have rows
} // end second if have rows
} // end first while have rows
} // end first if have rows
for more information see the nested loop section of this page http://www.advancedcustomfields.com/resources/have_rows/
