For my environment, I narrowed the issue down to the ACF core update alone (no other changes to WP and ACF add-on versions).
Working:
WP 3.6.1
ACF 4.2.2
ACF:Flexible Content Field 1.0.2
ACF:Repeater Field 1.0.1
ACF Repeater Collapser 1.1.0
ACF Support for Custom Post Templates 1.0
Custom Post Templates 1.5
Status after updating:
ACF 4.2.2 -> 4.3.0 :
Page renders differently as described in earlier post. has_sub_field returning false for specified repeater field.
Status after manual rollback:
ACF 4.3.0 -> 4.2.2 :
Page returns to expected rendering.
