The check boxes, are they Episerver properties? Can you share some code?

What version are you running on Episerver?

Sorry for not supplying any code samples. I hoped it would be needed. 

Its EPiServer CMS 9 and its an EPiServer property.

Here is the code:

The model

        [UIHint(CustomUiHints.SubscriptionPageSelector)]
        public virtual string SubscriptionPages { get; set; }

The  C# code that creates the checkboxes

    [EditorDescriptorRegistration(TargetType = typeof(string), UIHint = CustomUiHints.SubscriptionPageSelector)]
    public class SubscriptionPageEditorDescriptor : EditorDescriptor
    {
        public override void ModifyMetadata(ExtendedMetadata metadata, IEnumerable<Attribute> attributes)
        {
            SelectionFactoryType = typeof(SubscriptionPageSelectionFactory);
            ClientEditingClass = "epi-cms.contentediting.editors.CheckBoxListEditor";
            base.ModifyMetadata(metadata, attributes);
        }
    }

    public class SubscriptionPageSelectionFactory : ISelectionFactory
    {
        public IEnumerable<ISelectItem> GetSelections(ExtendedMetadata metadata)
        {
            var subscriptionPages = new List<SelectItem>();
            var subscriptions = ...GetSubscriptions
            foreach (var sub in subscriptions)
            {
                subscriptionPages.Add(new SelectItem() { Value = sub.Value, Text = sub.Key });
            }
            return subscriptionPages;
        }
    }

The CustomUIHints files

public const string SubscriptionPageSelector = "SubscriptionPageSelector";

The code is runned inside a scheduledJob. 

The xml structure is as in the picture. (if the picture is not visible then go to this url: http://tinypic.com/r/5aj09k/9 )

There is a container page that has children each child has the checkboxes. 

When retreving the values of the checkboxes the values are presented in a comma separated list, if the image is not visible, please refer to: http://postimg.org/image/phklg4dcn/

The information given above may be too much, in order to understand why the checkboxes arent preserving their state after publish. 

Note I have not created any controller og view for the model. Since the model will only be used to provide the checkbox list

Try changing

subscriptionPages.Add(new SelectItem() { Value = sub.Value, Text = sub.Key });

to 

subscriptionPages.Add(new SelectItem() { Value = sub.Value.ToString(), Text = sub.Key });

You're the man Daniel. 

That actually worked. 

Maybe you could throw in some few words about why that would do the trick.