I’m having exactly the same issue.
Currently developing a website in WP 4.3 using ACF 5.3.0.
When having site options with a nested repeater, only some of the field values are saved when clicking on save.
After having done some tests, i looks like the cause of this is a limitation of character for the field-name inside the nested repeaters.
for my case:
timeline_title (14chars did not save)
timelinetitle (13chars saved)
abcdefghijklm (13chars saved)
abcdefghijklmo (14chars did not save)
so a workaround until this gets fixed is to use a maximum of 13 characters for field-names.
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