In order to figure the issue out, I ran unserialize on both data strings and saw that the top example saved as an associative array like:
Need help with format of nested array in MySQL => Title 1
[point] => 55.635656,12.506767
and the second array was flat like:
[0] => title
[1] => Title 0
[2] => point
[3] => 8.228271, 56.094402
In order to have the imported example match the repeatable box, you need to replace
array_push($point,"title");
array_push($point,$newctexttitle);
array_push($point,"point");
with
$point['title'] = $newctexttitle;
and replace
array_push($point,$XYcoordinate);
with
$point['point'] = $XYcoordinate;
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