I am also facing the same issue. I was using ACF4. And, issue arises with fields in Repeater and Flexible fields. Then I upgraded to ACF Pro. Still issue was same. So, I changed a field from ACF-Qtranslate to Text, and it works fine.
My current environment:
– WordPress 4.2.2
– Advanced Custom Fields Pro 5.2.7
– qTranslate-X 3.3
– Advanced Custom Fields: qTranslate 1.7.9
Fields are still not saving.