Multiple dependencies are saving back to database (from chart) without commas between dependencies. When reloaded of course the dependencies didn't work. Added a comma before save back to database fixed the problem.
In tiki/lib/wiki-plugins/wikiplugin_ganttchart.php line 616 (or so) change:
$dependsIds .= $index;
$dependsIds .= ($index == '') ? $index : ','.$index;
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