If you have many images in the post you are likely to see this issue.
I had a case when:
Gallery 1 - image 1 - id=10
Gallery 2 - image 2 - id=110
But when I've opened the Gallery setup window from Gallery 1 both files were marked as selected.
this was caused due to the use of indexOf() JS function.
I've changed multiple-galleries.js as follow:
var $include = '', $is_update = false, $is_checked, $include_arr;
line 36 - added:
$include_arr = $include.split(", ");
if ($include != null && $include.indexOf($imgid) != -1)
if ($include_arr != null && jQuery.inArray($imgid, $include_arr) != -1)
And that's it - problem solved!
Hope you will fix this in the next release.