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Super common but highly annoying problem.
The checkboxes are stored densely in the array, where all other values end up in a sparse array.
So typically you store the ID value in the checkbox, and process array based on list of IDs, not positional.
Or you pre-process your checkbox array to match the rest of them.
Sorry for lack of coding examples, but hopefully that will get you going. Plenty of examples about the place - check out Denes Kubicek's sample application.